From 5825e51cf95e2cf98d08ce3c8279b2385c1c9b8f Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Wed, 14 Aug 2024 12:51:18 -0600 Subject: [PATCH 01/31] Update viz doc to clarify its current status (partial functionality - incompatible with OA API changes) (#540) Co-authored-by: Jessica Scheick --- .../IS2_data_visualization.ipynb | 20 +++++++++++++------ icepyx/core/visualization.py | 13 ++++++++---- 2 files changed, 23 insertions(+), 10 deletions(-) diff --git a/doc/source/example_notebooks/IS2_data_visualization.ipynb b/doc/source/example_notebooks/IS2_data_visualization.ipynb index 0f2819862..6d74e0865 100644 --- a/doc/source/example_notebooks/IS2_data_visualization.ipynb +++ b/doc/source/example_notebooks/IS2_data_visualization.ipynb @@ -7,7 +7,14 @@ "source": [ "# Visualizing ICESat-2 Elevations\n", "\n", - "This notebook ({nb-download}`download `) demonstrates interactive ICESat-2 elevation visualization by requesting data from [OpenAltimetry](https://www.openaltimetry.org/) based on metadata provided by [icepyx](https://icepyx.readthedocs.io/en/latest/). We will show how to plot spatial extent and elevation interactively. " + "This notebook ({nb-download}`download `) demonstrates interactive ICESat-2 elevation visualization by requesting data from [OpenAltimetry](https://www.openaltimetry.org/) based on metadata provided by [icepyx](https://icepyx.readthedocs.io/en/latest/). We will show how to plot spatial extent and elevation interactively.\n", + "\n", + "> ⚠️ **Some of this notebook is currently non-functional**\n", + ">\n", + "> Visualizations requiring the\n", + "> [OpenAltimetry API](https://openaltimetry.earthdatacloud.nasa.gov/data/openapi/swagger-ui/index.html)\n", + "> are currently unavailable (since ~October 2023).\n", + "> The API changed and we haven't yet updated this notebook correspondingly." ] }, { @@ -33,7 +40,7 @@ "id": "57f2cfd8", "metadata": {}, "source": [ - "Create an ICESat-2 query object\n", + "## Create an ICESat-2 query object\n", "\n", "Set the desired parameters for your data visualization.\n", "\n", @@ -148,6 +155,7 @@ "execution_count": null, "id": "93a712af-ab1f-4d79-834d-c2735a5677a8", "metadata": { + "scrolled": true, "tags": [] }, "outputs": [], @@ -222,16 +230,16 @@ "### Alternative Access Options to Visualize ICESat-2 elevation using OpenAltimetry API\n", "\n", "You can also view elevation data by importing the visualization module directly and initializing it with your query object or a list of parameters:\n", - " ```\n", + " ```python\n", " from icepyx.core.visualization import Visualize\n", " ```\n", " - passing your query object directly to the visualization module\n", - " ```\n", + " ```python\n", " region2 = ipx.Query(short_name, spatial_extent, date_range)\n", " vis = Visualize(region2)\n", " ```\n", " - creating a visualization object directly without first creating a query object\n", - " ```\n", + " ```python\n", " vis = Visualize(product=short_name, spatial_extent=spatial_extent, date_range=date_range)\n", " ```" ] @@ -264,7 +272,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.12.4" } }, "nbformat": 4, diff --git a/icepyx/core/visualization.py b/icepyx/core/visualization.py index bdbc6d2d9..5df884e2d 100644 --- a/icepyx/core/visualization.py +++ b/icepyx/core/visualization.py @@ -312,7 +312,13 @@ def make_request(self, base_url, payload): -------- request_OA_data """ - return requests.get(base_url, params=payload) + response = requests.get(base_url, params=payload) + if not response.ok: + raise RuntimeError( + f"Status {response.status_code} requesting url {response.request.url}" + ) + + return response def request_OA_data(self, paras) -> da.array: """ @@ -331,9 +337,8 @@ def request_OA_data(self, paras) -> da.array: """ warnings.warn( - "NOTICE: visualizations requiring the OpenAltimetry API are currently (October 2023) " - "unavailable while hosting of OpenAltimetry transitions from UCSD to NSIDC." - "A ticket has been issued to restore programmatic API access." + "NOTICE: visualizations requiring the OpenAltimetry API are currently" + " (August 2024) unavailable until we can adapt to API changes." ) base_url = "http://openaltimetry.earthdatacloud.nasa.gov/data/api/icesat2" From 46485517cb10494aee1e38dc7585dff0fd13419b Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Fri, 16 Aug 2024 12:14:46 -0600 Subject: [PATCH 02/31] Avoid running tests that require creds on PRs (#563) enables PRs from forks to pass CI tests and be merged --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index b3d7081e7..271eb5bff 100644 --- a/.travis.yml +++ b/.travis.yml @@ -27,7 +27,7 @@ stages: jobs: include: - stage: basic tests - script: pytest icepyx/ --verbose --cov app --ignore icepyx/tests/test_behind_NSIDC_API_login.py + script: pytest icepyx/ --verbose --cov app --ignore=icepyx/tests/test_behind_NSIDC_API_login.py --ignore=icepyx/tests/test_auth.py # includes an integrity check of the uploader as recommended by CodeCov after_success: - curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --keyring trustedkeys.gpg --import # One-time step @@ -41,4 +41,4 @@ jobs: - stage: behind Earthdata script: - export EARTHDATA_PASSWORD=$NSIDC_LOGIN - - pytest icepyx/tests/test_behind_NSIDC_API_login.py + - pytest icepyx/tests/test_behind_NSIDC_API_login.py icepyx/tests/test_auth.py From b0bb832b23299cbd38277327c4e23d7a20002654 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Fri, 16 Aug 2024 12:39:24 -0600 Subject: [PATCH 03/31] Skip linting and formatting Jupyter Notebooks for now (#567) Co-authored-by: Jessica Scheick --- .pre-commit-config.yaml | 2 +- pyproject.toml | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 62fe68370..f0b1de416 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,7 +11,7 @@ repos: args: [--markdown-linebreak-ext=md] - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.5.7 + rev: v0.6.0 hooks: - id: ruff args: ["--fix", "--show-fixes"] diff --git a/pyproject.toml b/pyproject.toml index 4f4c0a88c..69114cdbb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,6 +61,12 @@ version_file = "_icepyx_version.py" version_file_template = 'version = "{version}"' local_scheme = "node-and-date" fallback_version = "unknown" + + +[tool.ruff] +# DevGoal: Lint and format all Jupyter Notebooks, remove below. +extend-exclude = ["*.ipynb"] + # [tool.ruff.format] # docstring-code-format = true # docstring-code-line-length = "dynamic" From 8b57fca58cbbf6878cc08fb3494165e716a301cb Mon Sep 17 00:00:00 2001 From: Christian Clauss Date: Fri, 16 Aug 2024 20:57:19 +0200 Subject: [PATCH 04/31] Keep GitHub Actions up to date with GitHub's Dependabot (#555) Co-authored-by: Jessica Scheick Co-authored-by: Matt Fisher --- .github/dependabot.yml | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 000000000..0b84a2431 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,13 @@ +# Keep GitHub Actions up to date with GitHub's Dependabot... +# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot +# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file#package-ecosystem +version: 2 +updates: + - package-ecosystem: github-actions + directory: / + groups: + github-actions: + patterns: + - "*" # Group all Actions updates into a single larger pull request + schedule: + interval: monthly From a259f9a08c5593e385add9351136b3c17284475f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 17 Aug 2024 07:36:20 -0600 Subject: [PATCH 05/31] Bump the github-actions group with 3 updates (#568) Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/get_pypi_stats.yml | 2 +- .github/workflows/publish_to_pypi.yml | 4 ++-- .github/workflows/traffic_action.yml | 4 ++-- .github/workflows/uml_action.yml | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/get_pypi_stats.yml b/.github/workflows/get_pypi_stats.yml index 3461ef953..3ff8d14ea 100644 --- a/.github/workflows/get_pypi_stats.yml +++ b/.github/workflows/get_pypi_stats.yml @@ -16,7 +16,7 @@ jobs: # Steps represent a sequence of tasks that will be executed as part of the job steps: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: ref: "traffic" diff --git a/.github/workflows/publish_to_pypi.yml b/.github/workflows/publish_to_pypi.yml index e7fadd774..bd633e877 100644 --- a/.github/workflows/publish_to_pypi.yml +++ b/.github/workflows/publish_to_pypi.yml @@ -22,13 +22,13 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: # fetch all history so that setuptools-scm works fetch-depth: 0 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: 3.9 diff --git a/.github/workflows/traffic_action.yml b/.github/workflows/traffic_action.yml index 97705285f..48db62741 100644 --- a/.github/workflows/traffic_action.yml +++ b/.github/workflows/traffic_action.yml @@ -17,13 +17,13 @@ jobs: # Steps represent a sequence of tasks that will be executed as part of the job steps: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: ref: "traffic" # Calculates traffic and clones and stores in CSV file - name: GitHub traffic - uses: sangonzal/repository-traffic-action@v0.1.4 + uses: sangonzal/repository-traffic-action@v0.1.5 env: TRAFFIC_ACTION_TOKEN: ${{ secrets.TRAFFIC_ACTION_TOKEN }} diff --git a/.github/workflows/uml_action.yml b/.github/workflows/uml_action.yml index b85885023..60c4e0cf0 100644 --- a/.github/workflows/uml_action.yml +++ b/.github/workflows/uml_action.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: ref: ${{ github.event.pull_request.head.ref }} - name: set up environment From 8ef252cddbf5b0563ce2fe5559ab78291172f0bd Mon Sep 17 00:00:00 2001 From: Christian Clauss Date: Sun, 18 Aug 2024 19:00:17 +0200 Subject: [PATCH 06/31] Add codespell spelling/typo linter and fix errors (#556) Co-authored-by: Matt Fisher --- .pre-commit-config.yaml | 7 +++++++ ATTRIBUTION.rst | 2 +- doc/source/community/resources/2020_IS2_HW.rst | 2 +- doc/source/contributing/icepyx_internals.rst | 2 +- .../example_notebooks/IS2_DEM_comparison_WIP.ipynb | 14 +++++++------- .../example_notebooks/IS2_cloud_data_access.ipynb | 2 +- doc/source/example_notebooks/IS2_data_access.ipynb | 4 ++-- .../example_notebooks/IS2_data_read-in.ipynb | 2 +- .../example_notebooks/IS2_data_variables.ipynb | 6 +++--- .../example_notebooks/IS2_data_visualization.ipynb | 2 +- icepyx/core/APIformatting.py | 6 +++--- icepyx/core/auth.py | 2 +- icepyx/core/query.py | 4 ++-- icepyx/core/read.py | 2 +- icepyx/core/variables.py | 8 ++++---- icepyx/quest/quest.py | 2 +- icepyx/tests/test_granules.py | 2 +- icepyx/tests/test_quest.py | 2 +- icepyx/tests/test_quest_argo.py | 2 +- pyproject.toml | 3 +++ 20 files changed, 43 insertions(+), 33 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f0b1de416..1d681dbed 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,6 +10,13 @@ repos: - id: trailing-whitespace args: [--markdown-linebreak-ext=md] + - repo: https://github.com/codespell-project/codespell + rev: v2.3.0 + hooks: + - id: codespell + additional_dependencies: + - tomli + - repo: https://github.com/astral-sh/ruff-pre-commit rev: v0.6.0 hooks: diff --git a/ATTRIBUTION.rst b/ATTRIBUTION.rst index 655a678db..a595e32d4 100644 --- a/ATTRIBUTION.rst +++ b/ATTRIBUTION.rst @@ -99,7 +99,7 @@ to identify core issues and propose solutions to challenges around software cred For software, current best practices (`e.g. `_) emphasize the importance of having a document such as this one to describe an individual community's policies for credit, authorship, and attribution. This document is an effort to describe icepyx's policies, with an awareness that they may change -to accomodate community growth, best practices, and feedback. +to accommodate community growth, best practices, and feedback. We do not attempt to identify contribution levels through the number of commits made to the repository (e.g. ``git shortlog -sne``) or active engagement on GitHub (e.g. through issues, discussions, and pull requests) and Discourse. diff --git a/doc/source/community/resources/2020_IS2_HW.rst b/doc/source/community/resources/2020_IS2_HW.rst index de7d50218..391820f1c 100644 --- a/doc/source/community/resources/2020_IS2_HW.rst +++ b/doc/source/community/resources/2020_IS2_HW.rst @@ -7,7 +7,7 @@ first virtual Hackweek held by the University of Washington. While originally planned as a five-day, in-person workshop, the event was shifted to a fully virtual/remote setting in light of stay-at-home orders and travel restrictions in place to curb the spread of COVID-19. -To accomodate multiple time zones and limit the daily duration of online tutorial sessions, the event was spread out over the course of ten days. +To accommodate multiple time zones and limit the daily duration of online tutorial sessions, the event was spread out over the course of ten days. The first week had three half-days of interactive tutorials/lectures. The second week had four days that included some interactive tutorials/lectures and scheduled times where instructors were available to help participants with a facilitated exploration of datasets and hands-on software development. diff --git a/doc/source/contributing/icepyx_internals.rst b/doc/source/contributing/icepyx_internals.rst index 61c3e8ccb..53909d8ae 100644 --- a/doc/source/contributing/icepyx_internals.rst +++ b/doc/source/contributing/icepyx_internals.rst @@ -13,7 +13,7 @@ by any modules that need an Earthdata login. **Property Access** -Even though they aren't explicity defined in the init method, properties +Even though they aren't explicitly defined in the init method, properties like ``.session`` are accessible on a Query object because they are inherited. The code that indicates this to Python is ``EarthdataAuthMixin.__init__(self)``. diff --git a/doc/source/example_notebooks/IS2_DEM_comparison_WIP.ipynb b/doc/source/example_notebooks/IS2_DEM_comparison_WIP.ipynb index bf1bc8af4..f6cef3494 100644 --- a/doc/source/example_notebooks/IS2_DEM_comparison_WIP.ipynb +++ b/doc/source/example_notebooks/IS2_DEM_comparison_WIP.ipynb @@ -81,7 +81,7 @@ "import shutil\n", "import h5py\n", "import xarray as xr\n", - "# depedencies\n", + "# dependencies\n", "import getpass\n", "#from topolib.subsetDat import subsetBBox;\n", "from topolib import icesat2_data\n", @@ -265,7 +265,7 @@ "metadata": {}, "source": [ "## Preprocess #2\n", - "- Convert data into geopandas dataframe, which allows for doing basing geospatial opertaions" + "- Convert data into geopandas dataframe, which allows for doing basing geospatial operations" ] }, { @@ -316,7 +316,7 @@ "metadata": {}, "outputs": [], "source": [ - "# dict containing data entries to retrive\n", + "# dict containing data entries to retrieve\n", "dataset_dict = {'land_segments':['delta_time','longitude','latitude','atl06_quality_summary','quality','terrain_flg'], 'land_segments/terrain':['h_te_best_fit']}" ] }, @@ -438,7 +438,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## We will use the TANDEM-X Global DEM for our comparison. The resolution of the globally avaialable product is 90 m, with *horizontal* and *vertical* accuracy better than 2 to 3 m.\n", + "## We will use the TANDEM-X Global DEM for our comparison. The resolution of the globally available product is 90 m, with *horizontal* and *vertical* accuracy better than 2 to 3 m.\n", "- TANDEM-X DEM for the region was downloaded and preprocessed, filtered using scripts from the [tandemx](https://github.com/dshean/tandemx) repository" ] }, @@ -741,7 +741,7 @@ "metadata": {}, "outputs": [], "source": [ - "### Save the geodataframe in the specified way as expected by Ames Stereo Pipline\n", + "### Save the geodataframe in the specified way as expected by Ames Stereo Pipeline\n", "icesat2_pc = '/home/jovyan/icesat2/icesat2_colombia_pc.csv' \n", "gdf_colombia_dem_extent[['latitude','longitude','h_te_best_fit']].to_csv(icesat2_pc,header=False,index=None)" ] @@ -761,7 +761,7 @@ "metadata": {}, "outputs": [], "source": [ - "### Save the geodataframe in the specified way as expected by Ames Stereo Pipline\n", + "### Save the geodataframe in the specified way as expected by Ames Stereo Pipeline\n", "icesat2_pc = '/home/jovyan/icesat2/icesat2_colombia_pc.csv'\n", "pc_rename_dict = {'latitude':'lat','longitude':'lon','h_te_best_fit':'height_above_datum'}\n", "gdf_colombia_dem_extent = gdf_colombia_dem_extent.rename(columns=pc_rename_dict)\n", @@ -867,7 +867,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "- We see that after coregistration, the bias reduces to an extent. Note that this is a very preliminary analysis, results will be better after filtering the ATL08 points based on quality metrics and finding truly static surfaces (snow free during acquisiton time of ICESat-2 points)" + "- We see that after coregistration, the bias reduces to an extent. Note that this is a very preliminary analysis, results will be better after filtering the ATL08 points based on quality metrics and finding truly static surfaces (snow free during acquisition time of ICESat-2 points)" ] }, { diff --git a/doc/source/example_notebooks/IS2_cloud_data_access.ipynb b/doc/source/example_notebooks/IS2_cloud_data_access.ipynb index 194e25210..3f448aa4b 100644 --- a/doc/source/example_notebooks/IS2_cloud_data_access.ipynb +++ b/doc/source/example_notebooks/IS2_cloud_data_access.ipynb @@ -352,7 +352,7 @@ "source": [ "### Some important caveats\n", "\n", - "While the cloud data reading is functional within icepyx, it is very slow. Approximate timing shows it takes ~6 minutes of load time per variable per file from s3. Because of this you will recieve a warning if you try to load either more than three variables or two files at once.\n", + "While the cloud data reading is functional within icepyx, it is very slow. Approximate timing shows it takes ~6 minutes of load time per variable per file from s3. Because of this you will receive a warning if you try to load either more than three variables or two files at once.\n", "\n", "The slow load speed is a demonstration of the many steps involved in making cloud data actionable - the data supply chain needs optimized source data, efficient low level data readers, and high level libraries which are enabled to use the fastest low level data readers. Not all of these pieces fully developed right now, but the progress being made it exciting and there is lots of room for contribution!" ] diff --git a/doc/source/example_notebooks/IS2_data_access.ipynb b/doc/source/example_notebooks/IS2_data_access.ipynb index 67f94a7e7..268a9a3b9 100644 --- a/doc/source/example_notebooks/IS2_data_access.ipynb +++ b/doc/source/example_notebooks/IS2_data_access.ipynb @@ -485,7 +485,7 @@ }, "source": [ "```{admonition} Important Authentication Update\n", - "Previously, icepyx required you to explicitly use the `.earthdata_login()` function to login. Running this function is deprecated and will result in an error, as icepyx will call the login function as needed. The user will still need to provide their credentials using one of the three methods decribed above.\n", + "Previously, icepyx required you to explicitly use the `.earthdata_login()` function to login. Running this function is deprecated and will result in an error, as icepyx will call the login function as needed. The user will still need to provide their credentials using one of the three methods described above.\n", "```" ] }, @@ -504,7 +504,7 @@ "\n", "#### More details about the configuration parameters\n", "`request_mode` is \"asynchronous\" by default, which allows concurrent requests to be queued and processed without the need for a continuous connection between you and the API endpoint.\n", - "In contrast, using a \"synchronous\" `request_mode` means that the request relies on a direct, continous connection between you and the API endpoint.\n", + "In contrast, using a \"synchronous\" `request_mode` means that the request relies on a direct, continuous connection between you and the API endpoint.\n", "Outputs are directly downloaded, or \"streamed\", to your working directory.\n", "For this tutorial, we will set the request mode to asynchronous.\n", "\n", diff --git a/doc/source/example_notebooks/IS2_data_read-in.ipynb b/doc/source/example_notebooks/IS2_data_read-in.ipynb index c20cfbc95..9cd61ac01 100644 --- a/doc/source/example_notebooks/IS2_data_read-in.ipynb +++ b/doc/source/example_notebooks/IS2_data_read-in.ipynb @@ -15,7 +15,7 @@ "\n", "### Motivation\n", "Most often, when you open a data file, you must specify the underlying data structure and how you'd like the information to be read in.\n", - "A simple example of this, for instance when opening a csv or similarly delimited file, is letting the software know if the data contains a header row, what the data type is (string, double, float, boolean, etc.) for each column, what the delimeter is, and which columns or rows you'd like to be loaded.\n", + "A simple example of this, for instance when opening a csv or similarly delimited file, is letting the software know if the data contains a header row, what the data type is (string, double, float, boolean, etc.) for each column, what the delimiter is, and which columns or rows you'd like to be loaded.\n", "Many ICESat-2 data readers are quite manual in nature, requiring that you accurately type out a list of string paths to the various data variables.\n", "\n", "icepyx simplifies this process by relying on its awareness of ICESat-2 specific data file variable storage structure.\n", diff --git a/doc/source/example_notebooks/IS2_data_variables.ipynb b/doc/source/example_notebooks/IS2_data_variables.ipynb index 90fa8500c..2263ea768 100644 --- a/doc/source/example_notebooks/IS2_data_variables.ipynb +++ b/doc/source/example_notebooks/IS2_data_variables.ipynb @@ -278,7 +278,7 @@ "user_expressions": [] }, "source": [ - "Now that you know how to create or access Variables the remainder of this notebook showcases the functions availble for building and modifying variables lists. Remember, the example shown below uses a Query object, but the same methods are available if you are using a Read object or a Variables object." + "Now that you know how to create or access Variables the remainder of this notebook showcases the functions available for building and modifying variables lists. Remember, the example shown below uses a Query object, but the same methods are available if you are using a Read object or a Variables object." ] }, { @@ -360,7 +360,7 @@ "### ICESat-2 data variables\n", "\n", "ICESat-2 data is natively stored in a nested file format called hdf5.\n", - "Much like a directory-file system on a computer, each variable (file) has a unique path through the heirarchy (directories) within the file.\n", + "Much like a directory-file system on a computer, each variable (file) has a unique path through the hierarchy (directories) within the file.\n", "Thus, some variables (e.g. `'latitude'`, `'longitude'`) have multiple paths (one for each of the six beams in most products).\n", "\n", "#### Determine what variables are available\n", @@ -887,7 +887,7 @@ "source": [ "#### Example 2.8: add all possible values for variables+paths\n", "Append all `longitude` paths and all variables/paths with keyword `high_rate`.\n", - "Simlarly to what is shown in Example 4, if you submit only one `append` call as `region_a.order_vars.append(var_list=['longitude'], keyword_list=['high_rate'])` rather than the two `append` calls shown below, you will only add the variable `longitude` and only paths containing `high_rate`, not ALL paths for `longitude` and ANY variables with `high_rate` in their path." + "Similarly to what is shown in Example 4, if you submit only one `append` call as `region_a.order_vars.append(var_list=['longitude'], keyword_list=['high_rate'])` rather than the two `append` calls shown below, you will only add the variable `longitude` and only paths containing `high_rate`, not ALL paths for `longitude` and ANY variables with `high_rate` in their path." ] }, { diff --git a/doc/source/example_notebooks/IS2_data_visualization.ipynb b/doc/source/example_notebooks/IS2_data_visualization.ipynb index 6d74e0865..1654a83d2 100644 --- a/doc/source/example_notebooks/IS2_data_visualization.ipynb +++ b/doc/source/example_notebooks/IS2_data_visualization.ipynb @@ -145,7 +145,7 @@ "\n", "**Note: this function currently only supports products `ATL06, ATL07, ATL08, ATL10, ATL12, ATL13`**\n", "\n", - "Now that we have produced an interactive map showing the spatial extent of ICESat-2 data to be requested from NSIDC using icepyx, what if we want to have a quick check on the ICESat-2 elevations we plan to download from NSIDC? [OpenAltimetry API](https://openaltimetry.org/data/swagger-ui/#/) provides a nice way to achieve this. By sending metadata (product, date, bounding box, trackId) of each ICESat-2 file to the API, it can return elevation data almost instantaneously. The major drawback is requests are limited to 5x5 degree spatial bounding box selection for most of the ICESat-2 L3A products [ATL06, ATL07, ATL08, ATL10, ATL12, ATL13](https://icesat-2.gsfc.nasa.gov/science/data-products). To solve this issue, if you input spatial extent exceeds the 5 degree maximum in either horizontal dimension, your input spatial extent will be splited into 5x5 degree lat/lon grids first, use icepyx to query the metadata of ICESat-2 files located in each grid, and send each request to OpenAltimetry. Data sampling rates are 1/50 for ATL06 and 1/20 for other products.\n", + "Now that we have produced an interactive map showing the spatial extent of ICESat-2 data to be requested from NSIDC using icepyx, what if we want to have a quick check on the ICESat-2 elevations we plan to download from NSIDC? [OpenAltimetry API](https://openaltimetry.org/data/swagger-ui/#/) provides a nice way to achieve this. By sending metadata (product, date, bounding box, trackId) of each ICESat-2 file to the API, it can return elevation data almost instantaneously. The major drawback is requests are limited to 5x5 degree spatial bounding box selection for most of the ICESat-2 L3A products [ATL06, ATL07, ATL08, ATL10, ATL12, ATL13](https://icesat-2.gsfc.nasa.gov/science/data-products). To solve this issue, if you input spatial extent exceeds the 5 degree maximum in either horizontal dimension, your input spatial extent will be split into 5x5 degree lat/lon grids first, use icepyx to query the metadata of ICESat-2 files located in each grid, and send each request to OpenAltimetry. Data sampling rates are 1/50 for ATL06 and 1/20 for other products.\n", "\n", "There are multiple ways to access icepyx's visualization module. This option assumes you are visualizing the data as part of a workflow that will result in a data download. Alternative options for accessing the OpenAltimetry-based visualization module directly are provided at the end of this example." ] diff --git a/icepyx/core/APIformatting.py b/icepyx/core/APIformatting.py index eb77c37e9..d660a642c 100644 --- a/icepyx/core/APIformatting.py +++ b/icepyx/core/APIformatting.py @@ -243,7 +243,7 @@ def poss_keys(self): @property def fmted_keys(self): """ - Returns the dictionary of formated keys associated with the + Returns the dictionary of formatted keys associated with the parameter object. """ return self._fmted_keys @@ -320,7 +320,7 @@ def check_req_values(self): if all(keys in self.fmted_keys.keys() for keys in reqkeys): assert all( self.fmted_keys.get(key, -9999) != -9999 for key in reqkeys - ), "One of your formated parameters is missing a value" + ), "One of your formatted parameters is missing a value" return True else: return False @@ -340,7 +340,7 @@ def check_values(self): if any(keys in self._fmted_keys.keys() for keys in spatial_keys): assert any( self.fmted_keys.get(key, -9999) != -9999 for key in spatial_keys - ), "One of your formated parameters is missing a value" + ), "One of your formatted parameters is missing a value" return True else: return False diff --git a/icepyx/core/auth.py b/icepyx/core/auth.py index 55e34fd7f..2b5e796dd 100644 --- a/icepyx/core/auth.py +++ b/icepyx/core/auth.py @@ -49,7 +49,7 @@ class EarthdataAuthMixin: def __init__(self, auth=None): self._auth = copy.deepcopy(auth) - # initializatin of session and s3 creds is not allowed because those are generated + # initialization of session and s3 creds is not allowed because those are generated # from the auth object self._session = None self._s3login_credentials = None diff --git a/icepyx/core/query.py b/icepyx/core/query.py index a57806501..c6f63d59a 100644 --- a/icepyx/core/query.py +++ b/icepyx/core/query.py @@ -450,7 +450,7 @@ def __str__(self): @property def dataset(self): """ - Legacy property included to provide depracation warning. + Legacy property included to provide deprecation warning. See Also -------- @@ -722,7 +722,7 @@ def order_vars(self): @property def granules(self): """ - Return the granules object, which provides the underlying funtionality for searching, ordering, + Return the granules object, which provides the underlying functionality for searching, ordering, and downloading granules for the specified product. Users are encouraged to use the built-in wrappers rather than trying to access the granules object themselves. diff --git a/icepyx/core/read.py b/icepyx/core/read.py index e6bfc40b7..437b059b9 100644 --- a/icepyx/core/read.py +++ b/icepyx/core/read.py @@ -164,7 +164,7 @@ def _confirm_proceed(): class Read(EarthdataAuthMixin): """ Data object to read ICESat-2 data into the specified formats. - Provides flexiblity for reading nested hdf5 files into common analysis formats. + Provides flexibility for reading nested hdf5 files into common analysis formats. Parameters ---------- diff --git a/icepyx/core/variables.py b/icepyx/core/variables.py index 87c2a94e8..b14ee1ed5 100644 --- a/icepyx/core/variables.py +++ b/icepyx/core/variables.py @@ -437,7 +437,7 @@ def append(self, defaults=False, var_list=None, beam_list=None, keyword_list=Non ---------- defaults : boolean, default False Include the variables in the default variable list. Defaults are defined per-data product. - When specified in conjuction with a var_list, default variables not on the user- + When specified in conjunction with a var_list, default variables not on the user- specified list will be added to the order. var_list : list of strings, default None @@ -451,8 +451,8 @@ def append(self, defaults=False, var_list=None, beam_list=None, keyword_list=Non For all other products, acceptable values are ['gt1l', 'gt1r', 'gt2l', 'gt2r', 'gt3l', 'gt3r']. keyword_list : list of strings, default None - A list of subdirectory names (keywords), from any heirarchy level within the data structure, to select variables within - the product that include that keyword in their path. A list of availble keywords can be obtained by + A list of subdirectory names (keywords), from any hierarchy level within the data structure, to select variables within + the product that include that keyword in their path. A list of available keywords can be obtained by entering `keyword_list=['']` into the function. Notes @@ -545,7 +545,7 @@ def remove(self, all=False, var_list=None, beam_list=None, keyword_list=None): For all other products, acceptable values are ['gt1l', 'gt1r', 'gt2l', 'gt2r', 'gt3l', 'gt3r']. keyword_list : list of strings, default None - A list of subdirectory names (keywords), from any heirarchy level within the data structure, to select variables within + A list of subdirectory names (keywords), from any hierarchy level within the data structure, to select variables within the product that include that keyword in their path. Notes diff --git a/icepyx/quest/quest.py b/icepyx/quest/quest.py index a7cf9be3c..872f962f8 100644 --- a/icepyx/quest/quest.py +++ b/icepyx/quest/quest.py @@ -157,7 +157,7 @@ def add_argo(self, params=["temperature"], presRange=None) -> None: # error handling? what happens when the user tries to re-query? def search_all(self, **kwargs): """ - Searches for requred dataset within platform (i.e. ICESat-2, Argo) of interest. + Searches for required dataset within platform (i.e. ICESat-2, Argo) of interest. Parameters ---------- diff --git a/icepyx/tests/test_granules.py b/icepyx/tests/test_granules.py index 4e12c0eb3..8b00ce91d 100644 --- a/icepyx/tests/test_granules.py +++ b/icepyx/tests/test_granules.py @@ -30,7 +30,7 @@ # region_a.avail_granules(ids=True) # add test that s3urls are gotten for ALL products (e.g. ATL15 was failing -# due to .nc extention instead of .h5)) +# due to .nc extension instead of .h5)) # DevNote: clearly there's a better way that doesn't make the function so long... diff --git a/icepyx/tests/test_quest.py b/icepyx/tests/test_quest.py index 2270bfa8b..e4964fd38 100644 --- a/icepyx/tests/test_quest.py +++ b/icepyx/tests/test_quest.py @@ -15,7 +15,7 @@ def quest_instance(scope="module", autouse=True): ########## PER-DATASET ADDITION TESTS ########## -# Paramaterize these add_dataset tests once more datasets are added +# Parameterize these add_dataset tests once more datasets are added def test_add_is2(quest_instance): # Add ATL06 as a test to QUEST diff --git a/icepyx/tests/test_quest_argo.py b/icepyx/tests/test_quest_argo.py index a31b52f78..f2c677e8d 100644 --- a/icepyx/tests/test_quest_argo.py +++ b/icepyx/tests/test_quest_argo.py @@ -244,4 +244,4 @@ def test_replace_presRange_download(argo_quest_instance): assert "salinity" in df.columns -# second pres range test where does have a higher max pressure because only the new data was presRange limited? +# second pressure range test where does have a higher max pressure because only the new data was presRange limited? diff --git a/pyproject.toml b/pyproject.toml index 69114cdbb..f345fb9b9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -71,6 +71,9 @@ extend-exclude = ["*.ipynb"] # docstring-code-format = true # docstring-code-line-length = "dynamic" +[tool.codespell] +ignore-words-list = "aas,socio-economic,toi" + [tool.ruff.lint] select = [ "E", # pycodestyle From 118d49a3135c358bbdf9b2b7dc278bb0cb1b49c2 Mon Sep 17 00:00:00 2001 From: Christian Clauss Date: Sun, 18 Aug 2024 19:09:36 +0200 Subject: [PATCH 07/31] Validate pyproject.toml (#557) Co-authored-by: Matt Fisher --- .pre-commit-config.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1d681dbed..dc1236159 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -24,6 +24,11 @@ repos: args: ["--fix", "--show-fixes"] - id: ruff-format + - repo: https://github.com/abravalheri/validate-pyproject + rev: v0.18 + hooks: + - id: validate-pyproject + ci: autoupdate_schedule: monthly From 687766dc2b78d470a0289722bd71cae27eb2882a Mon Sep 17 00:00:00 2001 From: Christian Clauss Date: Mon, 19 Aug 2024 20:34:24 +0200 Subject: [PATCH 08/31] Enable currently-ignored linting rules E721, E722, F403 (#573) --- icepyx/quest/dataset_scripts/__init__.py | 2 +- icepyx/quest/dataset_scripts/argo.py | 2 +- icepyx/quest/quest.py | 4 ++-- icepyx/tests/test_Earthdata.py | 2 +- icepyx/tests/test_quest.py | 8 ++++---- pyproject.toml | 12 ++---------- 6 files changed, 11 insertions(+), 19 deletions(-) diff --git a/icepyx/quest/dataset_scripts/__init__.py b/icepyx/quest/dataset_scripts/__init__.py index 7834127ff..498059021 100644 --- a/icepyx/quest/dataset_scripts/__init__.py +++ b/icepyx/quest/dataset_scripts/__init__.py @@ -1 +1 @@ -from .dataset import * +from .dataset import * # noqa: F403 diff --git a/icepyx/quest/dataset_scripts/argo.py b/icepyx/quest/dataset_scripts/argo.py index b7f374bd6..3517a1440 100644 --- a/icepyx/quest/dataset_scripts/argo.py +++ b/icepyx/quest/dataset_scripts/argo.py @@ -477,7 +477,7 @@ def download(self, params=None, presRange=None, keep_existing=True) -> pd.DataFr profile_data = self._download_profile(i) profile_df = self._parse_into_df(profile_data[0]) merged_df = pd.concat([merged_df, profile_df], sort=False) - except: + except Exception: print("\tError processing profile {0}. Skipping.".format(i)) # now that we have a df from this round of downloads, we can add it to any existing dataframe diff --git a/icepyx/quest/quest.py b/icepyx/quest/quest.py index 872f962f8..4225d020a 100644 --- a/icepyx/quest/quest.py +++ b/icepyx/quest/quest.py @@ -187,7 +187,7 @@ def search_all(self, **kwargs): except KeyError: v.search_data() - except: + except Exception: dataset_name = type(v).__name__ print("Error querying data from {0}".format(dataset_name)) @@ -226,7 +226,7 @@ def download_all(self, path="", **kwargs): except KeyError: msg = v.download() print(msg) - except: + except Exception: dataset_name = type(v).__name__ print("Error downloading data from {0}".format(dataset_name)) diff --git a/icepyx/tests/test_Earthdata.py b/icepyx/tests/test_Earthdata.py index cfa2eb2c5..00ad87d8b 100644 --- a/icepyx/tests/test_Earthdata.py +++ b/icepyx/tests/test_Earthdata.py @@ -65,7 +65,7 @@ def earthdata_login(uid=None, pwd=None, email=None, s3token=False) -> bool: try: url = "urs.earthdata.nasa.gov" mock_uid, _, mock_pwd = netrc.netrc(netrc).authenticators(url) - except: + except Exception: mock_uid = os.environ.get("EARTHDATA_USERNAME") mock_pwd = os.environ.get("EARTHDATA_PASSWORD") diff --git a/icepyx/tests/test_quest.py b/icepyx/tests/test_quest.py index e4964fd38..19ad78432 100644 --- a/icepyx/tests/test_quest.py +++ b/icepyx/tests/test_quest.py @@ -26,9 +26,9 @@ def test_add_is2(quest_instance): obs = quest_instance.datasets - assert type(obs) == dict + assert type(obs) is dict assert exp_key in obs.keys() - assert type(obs[exp_key]) == exp_type + assert type(obs[exp_key]) is exp_type assert quest_instance.datasets[exp_key].product == prod @@ -40,9 +40,9 @@ def test_add_argo(quest_instance): obs = quest_instance.datasets - assert type(obs) == dict + assert type(obs) is dict assert exp_key in obs.keys() - assert type(obs[exp_key]) == exp_type + assert type(obs[exp_key]) is exp_type assert set(quest_instance.datasets[exp_key].params) == set(params) diff --git a/pyproject.toml b/pyproject.toml index f345fb9b9..ef8efde88 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,6 +62,8 @@ version_file_template = 'version = "{version}"' local_scheme = "node-and-date" fallback_version = "unknown" +[tool.codespell] +ignore-words-list = "aas,socio-economic,toi" [tool.ruff] # DevGoal: Lint and format all Jupyter Notebooks, remove below. @@ -71,9 +73,6 @@ extend-exclude = ["*.ipynb"] # docstring-code-format = true # docstring-code-line-length = "dynamic" -[tool.codespell] -ignore-words-list = "aas,socio-economic,toi" - [tool.ruff.lint] select = [ "E", # pycodestyle @@ -87,13 +86,6 @@ ignore = [ # overlong comments. # See: https://github.com/psf/black/issues/1713#issuecomment-1357045092 "E501", - # TODO: remove ignores below this line - # comparison syntax in tests - "E721", - # bare except - "E722", - # unable to detect undefined names - "F403", ] [tool.ruff.lint.per-file-ignores] From 3c06edba405e61113c33e3756bf13f5c20f3122c Mon Sep 17 00:00:00 2001 From: Christian Clauss Date: Mon, 19 Aug 2024 21:02:45 +0200 Subject: [PATCH 09/31] Add ruff rules C4 to check comprehensions (#570) --- doc/sphinxext/announce.py | 2 +- icepyx/core/APIformatting.py | 2 +- icepyx/core/granules.py | 2 +- icepyx/core/read.py | 12 ++++++------ icepyx/tests/test_auth.py | 4 +--- pyproject.toml | 1 + 6 files changed, 11 insertions(+), 12 deletions(-) diff --git a/doc/sphinxext/announce.py b/doc/sphinxext/announce.py index 6ff0e4884..6c2069e4d 100644 --- a/doc/sphinxext/announce.py +++ b/doc/sphinxext/announce.py @@ -125,7 +125,7 @@ def get_authors(revision_range): # pre.discard("Homu") # Append '+' to new authors. - authors = [s + " +" for s in cur - pre] + [s for s in cur & pre] + authors = [s + " +" for s in cur - pre] + list(cur & pre) authors.sort() return authors diff --git a/icepyx/core/APIformatting.py b/icepyx/core/APIformatting.py index d660a642c..d18ee7990 100644 --- a/icepyx/core/APIformatting.py +++ b/icepyx/core/APIformatting.py @@ -298,7 +298,7 @@ def _check_valid_keys(self): # if self._wanted == None: # raise ValueError("No desired parameter list was passed") - val_list = list(set(val for lis in self.poss_keys.values() for val in lis)) + val_list = list({val for lis in self.poss_keys.values() for val in lis}) for key in self.fmted_keys.keys(): assert key in val_list, ( diff --git a/icepyx/core/granules.py b/icepyx/core/granules.py index 205149f56..b5836e2c3 100644 --- a/icepyx/core/granules.py +++ b/icepyx/core/granules.py @@ -82,7 +82,7 @@ def gran_IDs(grans, ids=False, cycles=False, tracks=False, dates=False, cloud=Fa except KeyError: pass - if any([param is True for param in [cycles, tracks, dates]]): + if any(param is True for param in [cycles, tracks, dates]): # PRD: ICESat-2 product # HEM: Sea Ice Hemisphere flag # YY,MM,DD,HH,MN,SS: Year, Month, Day, Hour, Minute, Second diff --git a/icepyx/core/read.py b/icepyx/core/read.py index 437b059b9..088656abc 100644 --- a/icepyx/core/read.py +++ b/icepyx/core/read.py @@ -661,11 +661,11 @@ def _build_dataset_template(self, file): """ is2ds = xr.Dataset( - coords=dict( - gran_idx=[np.uint64(999999)], - source_file=(["gran_idx"], [file]), - ), - attrs=dict(data_product=self.product), + coords={ + "gran_idx": [np.uint64(999999)], + "source_file": (["gran_idx"], [file]), + }, + attrs={"data_product": self.product}, ) return is2ds @@ -740,7 +740,7 @@ def _build_single_file_dataset(self, file, groups_list): "ATL23", ]: wanted_grouponly_set = set(wanted_groups_tiered[0]) - wanted_groups_list = list(sorted(wanted_grouponly_set)) + wanted_groups_list = sorted(wanted_grouponly_set) if len(wanted_groups_list) == 1: is2ds = self._read_single_grp(file, grp_path=wanted_groups_list[0]) else: diff --git a/icepyx/tests/test_auth.py b/icepyx/tests/test_auth.py index 50ae1e6ca..9b720a0f8 100644 --- a/icepyx/tests/test_auth.py +++ b/icepyx/tests/test_auth.py @@ -23,9 +23,7 @@ def test_get_session(auth_instance): # Test that .s3login_credentials creates a dict with the correct keys def test_get_s3login_credentials(auth_instance): assert isinstance(auth_instance.s3login_credentials, dict) - expected_keys = set( - ["accessKeyId", "secretAccessKey", "sessionToken", "expiration"] - ) + expected_keys = {"accessKeyId", "secretAccessKey", "sessionToken", "expiration"} assert set(auth_instance.s3login_credentials.keys()) == expected_keys diff --git a/pyproject.toml b/pyproject.toml index ef8efde88..9d6e2f6e4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -75,6 +75,7 @@ extend-exclude = ["*.ipynb"] [tool.ruff.lint] select = [ + "C4", # flake8-comprehensions "E", # pycodestyle "F", # pyflakes ] From fca67b9f89019906ce921f61b64c23211f0fb0ec Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 20 Aug 2024 16:53:46 -0600 Subject: [PATCH 10/31] Bugfix: catch multiple types of exceptions (#560) --- icepyx/core/query.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/icepyx/core/query.py b/icepyx/core/query.py index c6f63d59a..8e12e4388 100644 --- a/icepyx/core/query.py +++ b/icepyx/core/query.py @@ -870,7 +870,7 @@ def show_custom_options(self, dictview=False): try: all(key in self._cust_options.keys() for key in keys) - except AttributeError or KeyError: + except (AttributeError, KeyError): self._cust_options = is2ref._get_custom_options( self.session, self.product, self._version ) From 6c6366aa004f4f33821348efff815a9d35650565 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Wed, 21 Aug 2024 15:18:49 -0600 Subject: [PATCH 11/31] Add quickstart to README (#549) Co-authored-by: Jessica Scheick --- README.rst | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/README.rst b/README.rst index 5240a1113..5ef8b1ba7 100644 --- a/README.rst +++ b/README.rst @@ -85,6 +85,32 @@ Alternatively, you can also install icepyx using `pip Date: Fri, 23 Aug 2024 03:19:19 +0200 Subject: [PATCH 12/31] Add ruff rules SIM to simplify Python code (#572) --- doc/sphinxext/announce.py | 5 +---- icepyx/core/APIformatting.py | 14 +++++++------- icepyx/core/auth.py | 8 +++----- icepyx/core/granules.py | 7 +++---- icepyx/core/query.py | 16 +++++++--------- icepyx/core/read.py | 2 +- icepyx/core/spatial.py | 7 ++----- icepyx/core/variables.py | 19 ++++++------------- icepyx/quest/dataset_scripts/argo.py | 9 +++------ icepyx/quest/quest.py | 2 +- icepyx/tests/test_Earthdata.py | 5 +---- icepyx/tests/test_behind_NSIDC_API_login.py | 4 ++-- icepyx/tests/test_quest.py | 6 +++--- pyproject.toml | 2 ++ 14 files changed, 42 insertions(+), 64 deletions(-) diff --git a/doc/sphinxext/announce.py b/doc/sphinxext/announce.py index 6c2069e4d..e053f4b62 100644 --- a/doc/sphinxext/announce.py +++ b/doc/sphinxext/announce.py @@ -77,10 +77,7 @@ def get_authors(revision_range): # e.g. v1.0.1|HEAD maybe_tag, head = cur_release.split("|") assert head == "HEAD" - if maybe_tag in this_repo.tags: - cur_release = maybe_tag - else: - cur_release = head + cur_release = maybe_tag if maybe_tag in this_repo.tags else head revision_range = f"{lst_release}..{cur_release}" # authors, in current release and previous to current release. diff --git a/icepyx/core/APIformatting.py b/icepyx/core/APIformatting.py index d18ee7990..90b7f3ac6 100644 --- a/icepyx/core/APIformatting.py +++ b/icepyx/core/APIformatting.py @@ -73,7 +73,7 @@ def _fmt_readable_granules(dset, **kwds): # list of readable granule names readable_granule_list = [] # if querying either by 91-day orbital cycle or RGT - if "cycles" in kwargs.keys() or "tracks" in kwargs.keys(): + if "cycles" in kwargs or "tracks" in kwargs: # default character wildcards for cycles and tracks kwargs.setdefault("cycles", ["??"]) kwargs.setdefault("tracks", ["????"]) @@ -110,7 +110,7 @@ def _fmt_var_subset_list(vdict): """ subcover = "" - for vn in vdict.keys(): + for vn in vdict: vpaths = vdict[vn] for vpath in vpaths: subcover += "/" + vpath + "," @@ -300,7 +300,7 @@ def _check_valid_keys(self): val_list = list({val for lis in self.poss_keys.values() for val in lis}) - for key in self.fmted_keys.keys(): + for key in self.fmted_keys: assert key in val_list, ( "An invalid key (" + key + ") was passed. Please remove it using `del`" ) @@ -317,7 +317,7 @@ def check_req_values(self): ), "You cannot call this function for your parameter type" reqkeys = self.poss_keys[self._reqtype] - if all(keys in self.fmted_keys.keys() for keys in reqkeys): + if all(keys in self.fmted_keys for keys in reqkeys): assert all( self.fmted_keys.get(key, -9999) != -9999 for key in reqkeys ), "One of your formatted parameters is missing a value" @@ -337,7 +337,7 @@ def check_values(self): spatial_keys = self.poss_keys["spatial"] # not the most robust check, but better than nothing... - if any(keys in self._fmted_keys.keys() for keys in spatial_keys): + if any(keys in self._fmted_keys for keys in spatial_keys): assert any( self.fmted_keys.get(key, -9999) != -9999 for key in spatial_keys ), "One of your formatted parameters is missing a value" @@ -410,13 +410,13 @@ def build_params(self, **kwargs): opt_keys = self.poss_keys["optional"] for key in opt_keys: - if key == "Coverage" and key in kwargs.keys(): + if key == "Coverage" and key in kwargs: # DevGoal: make there be an option along the lines of Coverage=default, which will get the default variables for that product without the user having to input is2obj.build_wanted_wanted_var_list as their input value for using the Coverage kwarg self._fmted_keys.update( {key: _fmt_var_subset_list(kwargs[key])} ) elif (key == "temporal" or key == "time") and ( - "start" in kwargs.keys() and "end" in kwargs.keys() + "start" in kwargs and "end" in kwargs ): self._fmted_keys.update( _fmt_temporal(kwargs["start"], kwargs["end"], key) diff --git a/icepyx/core/auth.py b/icepyx/core/auth.py index 2b5e796dd..8e263e730 100644 --- a/icepyx/core/auth.py +++ b/icepyx/core/auth.py @@ -107,11 +107,9 @@ def set_s3_creds(): # Only generate s3login_credentials the first time credentials are accessed, or if an hour # has passed since the last login - if self._s3login_credentials is None: - set_s3_creds() - elif (datetime.datetime.now() - self._s3_initial_ts) >= datetime.timedelta( - hours=1 - ): + if self._s3login_credentials is None or ( + datetime.datetime.now() - self._s3_initial_ts + ) >= datetime.timedelta(hours=1): set_s3_creds() return self._s3login_credentials diff --git a/icepyx/core/granules.py b/icepyx/core/granules.py index b5836e2c3..2c51e208b 100644 --- a/icepyx/core/granules.py +++ b/icepyx/core/granules.py @@ -75,10 +75,9 @@ def gran_IDs(grans, ids=False, cycles=False, tracks=False, dates=False, cloud=Fa if cloud is True: try: for link in gran["links"]: - if link["href"].startswith("s3") and link["href"].endswith( - (".h5", "nc") - ): - gran_s3urls.append(link["href"]) + href = link["href"] + if href.startswith("s3") and href.endswith((".h5", "nc")): + gran_s3urls.append(href) except KeyError: pass diff --git a/icepyx/core/query.py b/icepyx/core/query.py index 8e12e4388..ed241662b 100644 --- a/icepyx/core/query.py +++ b/icepyx/core/query.py @@ -126,7 +126,7 @@ def __init__( **kwargs, ): # validate & init spatial extent - if "xdateline" in kwargs.keys(): + if "xdateline" in kwargs: self._spatial = spat.Spatial(spatial_extent, xdateline=kwargs["xdateline"]) else: self._spatial = spat.Spatial(spatial_extent) @@ -637,7 +637,7 @@ def subsetparams(self, **kwargs): else: # If the user has supplied a subset list of variables, append the # icepyx required variables to the Coverage dict - if "Coverage" in kwargs.keys(): + if "Coverage" in kwargs: var_list = [ "orbit_info/sc_orient", "orbit_info/sc_orient_time", @@ -653,7 +653,7 @@ def subsetparams(self, **kwargs): ] # Add any variables from var_list to Coverage that are not already included for var in var_list: - if var not in kwargs["Coverage"].keys(): + if var not in kwargs["Coverage"]: kwargs["Coverage"][var.split("/")[-1]] = [var] if self._subsetparams is None: @@ -741,9 +741,7 @@ def granules(self): """ - if not hasattr(self, "_granules"): - self._granules = Granules() - elif self._granules is None: + if not hasattr(self, "_granules") or self._granules is None: self._granules = Granules() return self._granules @@ -869,7 +867,7 @@ def show_custom_options(self, dictview=False): ] try: - all(key in self._cust_options.keys() for key in keys) + all(key in self._cust_options for key in keys) except (AttributeError, KeyError): self._cust_options = is2ref._get_custom_options( self.session, self.product, self._version @@ -999,7 +997,7 @@ def order_granules(self, verbose=False, subset=True, email=False, **kwargs): if self._reqparams._reqtype == "search": self._reqparams._reqtype = "download" - if "email" in self._reqparams.fmted_keys.keys() or email is False: + if "email" in self._reqparams.fmted_keys or email is False: self._reqparams.build_params(**self._reqparams.fmted_keys) elif email is True: user_profile = self.auth.get_user_profile() @@ -1022,7 +1020,7 @@ def order_granules(self, verbose=False, subset=True, email=False, **kwargs): self.granules # Place multiple orders, one per granule, if readable_granule_name is used. - if "readable_granule_name[]" in self.CMRparams.keys(): + if "readable_granule_name[]" in self.CMRparams: gran_name_list = self.CMRparams["readable_granule_name[]"] tempCMRparams = self.CMRparams if len(gran_name_list) > 1: diff --git a/icepyx/core/read.py b/icepyx/core/read.py index 088656abc..28da685d7 100644 --- a/icepyx/core/read.py +++ b/icepyx/core/read.py @@ -120,7 +120,7 @@ def _parse_source(data_source, glob_kwargs={}) -> list: # if data_source is a directory glob search the directory and assign to _filelist data_source = os.path.join(data_source, "*") filelist = glob.glob(data_source, **glob_kwargs) - elif isinstance(data_source, str) or isinstance(data_source, Path): + elif isinstance(data_source, (Path, str)): if data_source.startswith("s3"): # if the string is an s3 path put it in the _filelist without globbing filelist = [data_source] diff --git a/icepyx/core/spatial.py b/icepyx/core/spatial.py index d810726b3..650ca06be 100644 --- a/icepyx/core/spatial.py +++ b/icepyx/core/spatial.py @@ -496,7 +496,7 @@ def __init__(self, spatial_extent, **kwarg): self._spatial_ext = [float(i) for i in arrpoly] # check for cross dateline keyword submission - if "xdateline" in kwarg.keys(): + if "xdateline" in kwarg: self._xdateln = kwarg["xdateline"] assert self._xdateln in [ True, @@ -542,10 +542,7 @@ def extent_as_gdf(self): """ # TODO: test this - if hasattr(self, "_xdateln"): - xdateln = self._xdateln - else: - xdateln = None + xdateln = self._xdateln if hasattr(self, "_xdateln") else None if not hasattr(self, "_gdf_spat"): if self._geom_file is not None: diff --git a/icepyx/core/variables.py b/icepyx/core/variables.py index b14ee1ed5..bf4a38c66 100644 --- a/icepyx/core/variables.py +++ b/icepyx/core/variables.py @@ -84,10 +84,7 @@ def __init__( self._path = val.check_s3bucket(path) # Set up auth - if self._path.startswith("s3"): - auth = self.auth - else: - auth = None + auth = self.auth if self._path.startswith("s3") else None # Read the product and version from the file self._product = is2ref.extract_product(self._path, auth=auth) self._version = is2ref.extract_version(self._path, auth=auth) @@ -111,11 +108,7 @@ def __init__( @property def path(self): - if self._path: - path = self._path - else: - path = None - return path + return self._path if self._path else None @property def product(self): @@ -271,7 +264,7 @@ def parse_var_list(varlist, tiered=True, tiered_vars=False): for vn in varlist: vpath, vkey = os.path.split(vn) # print('path '+ vpath + ', key '+vkey) - if vkey not in vgrp.keys(): + if vkey not in vgrp: vgrp[vkey] = [vn] else: vgrp[vkey].append(vn) @@ -321,7 +314,7 @@ def _check_valid_lists( # check if the list of variables, if specified, are available in the product if var_list is not None: for var_id in var_list: - if var_id not in vgrp.keys(): + if var_id not in vgrp: err_msg_varid = "Invalid variable name: " + var_id + ". " err_msg_varid = err_msg_varid + "Please select from this list: " err_msg_varid = err_msg_varid + ", ".join(vgrp.keys()) @@ -514,9 +507,9 @@ def append(self, defaults=False, var_list=None, beam_list=None, keyword_list=Non ) # update the data object variables - for vkey in final_vars.keys(): + for vkey in final_vars: # add all matching keys and paths for new variables - if vkey not in self.wanted.keys(): + if vkey not in self.wanted: self.wanted[vkey] = final_vars[vkey] else: for vpath in final_vars[vkey]: diff --git a/icepyx/quest/dataset_scripts/argo.py b/icepyx/quest/dataset_scripts/argo.py index 3517a1440..b170feec0 100644 --- a/icepyx/quest/dataset_scripts/argo.py +++ b/icepyx/quest/dataset_scripts/argo.py @@ -45,10 +45,7 @@ def __init__(self, aoi, toi, params=["temperature"], presRange=None): self._apikey = "92259861231b55d32a9c0e4e3a93f4834fc0b6fa" def __str__(self): - if self.presRange is None: - prange = "All" - else: - prange = str(self.presRange) + prange = "All" if self.presRange is None else str(self.presRange) if self.argodata is None: df = "No data yet" @@ -297,7 +294,7 @@ def search_data(self, params=None, presRange=None, printURL=False) -> str: selectionProfiles = resp.json() # Consider any status other than 2xx an error - if not resp.status_code // 100 == 2: + if resp.status_code // 100 != 2: # check for the existence of profiles from query if selectionProfiles == []: msg = ( @@ -362,7 +359,7 @@ def _download_profile( print(resp.url) # Consider any status other than 2xx an error - if not resp.status_code // 100 == 2: + if resp.status_code // 100 != 2: return "Error: Unexpected response {}".format(resp) profile = resp.json() return profile diff --git a/icepyx/quest/quest.py b/icepyx/quest/quest.py index 4225d020a..b61376625 100644 --- a/icepyx/quest/quest.py +++ b/icepyx/quest/quest.py @@ -72,7 +72,7 @@ def __str__(self): if not self.datasets: str += "None" else: - for i in self.datasets.keys(): + for i in self.datasets: str += "{0}, ".format(i) str = str[:-2] # remove last ', ' diff --git a/icepyx/tests/test_Earthdata.py b/icepyx/tests/test_Earthdata.py index 00ad87d8b..06b0bc150 100644 --- a/icepyx/tests/test_Earthdata.py +++ b/icepyx/tests/test_Earthdata.py @@ -69,7 +69,4 @@ def earthdata_login(uid=None, pwd=None, email=None, s3token=False) -> bool: mock_uid = os.environ.get("EARTHDATA_USERNAME") mock_pwd = os.environ.get("EARTHDATA_PASSWORD") - if (uid == mock_uid) & (pwd == mock_pwd): - return True - else: - return False + return bool((uid == mock_uid) & (pwd == mock_pwd)) diff --git a/icepyx/tests/test_behind_NSIDC_API_login.py b/icepyx/tests/test_behind_NSIDC_API_login.py index 47d0a10d2..bf77da074 100644 --- a/icepyx/tests/test_behind_NSIDC_API_login.py +++ b/icepyx/tests/test_behind_NSIDC_API_login.py @@ -37,8 +37,8 @@ def test_get_custom_options_output(session): obs = is2ref._get_custom_options(session, "ATL06", "006") with open("./icepyx/tests/ATL06v06_options.json") as exp_json: exp = json.load(exp_json) - assert all(keys in obs.keys() for keys in exp.keys()) - assert all(obs[key] == exp[key] for key in exp.keys()) + assert all(keys in obs for keys in exp) + assert all(obs[key] == exp[key] for key in exp) ########## query module ########## diff --git a/icepyx/tests/test_quest.py b/icepyx/tests/test_quest.py index 19ad78432..1b8259aaa 100644 --- a/icepyx/tests/test_quest.py +++ b/icepyx/tests/test_quest.py @@ -27,7 +27,7 @@ def test_add_is2(quest_instance): obs = quest_instance.datasets assert type(obs) is dict - assert exp_key in obs.keys() + assert exp_key in obs assert type(obs[exp_key]) is exp_type assert quest_instance.datasets[exp_key].product == prod @@ -41,7 +41,7 @@ def test_add_argo(quest_instance): obs = quest_instance.datasets assert type(obs) is dict - assert exp_key in obs.keys() + assert exp_key in obs assert type(obs[exp_key]) is exp_type assert set(quest_instance.datasets[exp_key].params) == set(params) @@ -54,7 +54,7 @@ def test_add_multiple_datasets(quest_instance): # print(quest_instance.datasets["icesat2"].product) exp_keys = ["argo", "icesat2"] - assert set(exp_keys) == set(quest_instance.datasets.keys()) + assert set(exp_keys) == set(quest_instance.datasets) ########## ALL DATASET METHODS TESTS ########## diff --git a/pyproject.toml b/pyproject.toml index 9d6e2f6e4..66eb7b6f9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -78,6 +78,7 @@ select = [ "C4", # flake8-comprehensions "E", # pycodestyle "F", # pyflakes + "SIM", # flake8-simplify ] ignore = [ # Line too long @@ -87,6 +88,7 @@ ignore = [ # overlong comments. # See: https://github.com/psf/black/issues/1713#issuecomment-1357045092 "E501", + "SIM105", # suppressible-exception ] [tool.ruff.lint.per-file-ignores] From bc39b7ca4ecda92baed076ffa89096585aebe40d Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Thu, 22 Aug 2024 19:47:14 -0600 Subject: [PATCH 13/31] docs: add cclauss as a contributor for maintenance and review (#583) Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Matt Fisher --- .all-contributorsrc | 11 ++++ CONTRIBUTORS.rst | 123 ++++++++++++++++++++++---------------------- 2 files changed, 73 insertions(+), 61 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index c9e690f0e..715c4af76 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -470,6 +470,17 @@ "contributions": [ "ideas" ] + }, + { + "login": "cclauss", + "name": "Christian Clauss", + "avatar_url": "https://avatars.githubusercontent.com/u/3709715?v=4", + "profile": "https://github.com/cclauss", + "contributions": [ + "maintenance", + "review", + "tool" + ] } ], "contributorsPerLine": 7, diff --git a/CONTRIBUTORS.rst b/CONTRIBUTORS.rst index 5d5c4530c..04e227ce6 100644 --- a/CONTRIBUTORS.rst +++ b/CONTRIBUTORS.rst @@ -8,68 +8,69 @@ Thanks goes to these wonderful people (`emoji key - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Amy Steiker
Amy Steiker
💡 📖 🧑‍🏫		Anna Valentine
Anna Valentine
💡		Anthony Arendt
Anthony Arendt
🐛 💼 📋 🔍		Bruce Wallin
Bruce Wallin
💻 📖 🤔 👀 💬		David Shean
David Shean
🐛 🧑‍🏫		Don Setiawan
Don Setiawan
🚇 📦		Facundo Sapienza
Facundo Sapienza
💡 🐛
Fernando Perez
Fernando Perez
🎨 💼 🤔		JP Swinski
JP Swinski
💻 👀		Jessica
Jessica
🐛 💻 🖋 📖 🎨 💡 🤔 🚧 🧑‍🏫 📆 💬 👀		Joachim Meyer
Joachim Meyer
🧑‍🏫 🚧		Kelsey Bisson
Kelsey Bisson
🐛 💻 📖 🤔 💡 🤔 🧑‍🏫 💬 👀 ✅		Lindsey Heagy
Lindsey Heagy
🧑‍🏫 👀		Molly Wieringa
Molly Wieringa
🤔
Nicole Abib
Nicole Abib
💻 🤔		Rachel Wegener
Rachel Wegener
🐛 💻 📖 🤔 🚧 👀 ⚠️ ✅		Raphael Hagen
Raphael Hagen
📖 🎨 💻 🚇 👀		Romina Piunno
Romina Piunno
💻 🤔 🧑‍🏫 👀 ✅		Sarah Hall
Sarah Hall
🐛 💻 📖 🚧 ⚠️		Scott Henderson
Scott Henderson
🚧		Sebastian Alvis
Sebastian Alvis
📖 🚇
Shashank Bhushan
Shashank Bhushan
💡		Tian Li
Tian Li
🐛 💻 📖 💡 🤔 👀 ⚠️ 🔧		Tom Johnson
Tom Johnson
📖 🚇		Tyler Sutterley
Tyler Sutterley
📖 💻 🤔 💬 🛡️ ⚠️		Wei Ji
Wei Ji
🐛 💻 📖 💡 🤔 🚇 🚧 🧑‍🏫 💬 👀 ⚠️ 📢		Whyjay Zheng
Whyjay Zheng
✅ 🐛 💻 👀		Wilson Sauthoff
Wilson Sauthoff
👀
Zach Fair
Zach Fair
🐛 💻 📖 🤔 💬 👀 ✅		alexdibella
alexdibella
🐛 🤔 💻		bidhya
bidhya
💡		learn2phoenix
learn2phoenix
💻		liuzheng-arctic
liuzheng-arctic
📖 🐛 💻 🤔 👀 🔧 💡		nitin-ravinder
nitin-ravinder
🐛 👀		ravindraK08
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👀
rtilling
rtilling
🤔		smithb
smithb
🤔		tedmaksym
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🤔		trevorskaggs
trevorskaggs
🐛 💻		trey-stafford
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Amy Steiker
Amy Steiker
💡 📖 🧑‍🏫		Anna Valentine
Anna Valentine
💡		Anthony Arendt
Anthony Arendt
🐛 💼 📋 🔍		Bruce Wallin
Bruce Wallin
💻 📖 🤔 👀 💬		Christian Clauss
Christian Clauss
🚧 👀 🔧		David Shean
David Shean
🐛 🧑‍🏫		Don Setiawan
Don Setiawan
🚇 📦
Facundo Sapienza
Facundo Sapienza
💡 🐛		Fernando Perez
Fernando Perez
🎨 💼 🤔		JP Swinski
JP Swinski
💻 👀		Jessica
Jessica
🐛 💻 🖋 📖 🎨 💡 🤔 🚧 🧑‍🏫 📆 💬 👀		Joachim Meyer
Joachim Meyer
🧑‍🏫 🚧		Kelsey Bisson
Kelsey Bisson
🐛 💻 📖 🤔 💡 🤔 🧑‍🏫 💬 👀 ✅		Lindsey Heagy
Lindsey Heagy
🧑‍🏫 👀
Molly Wieringa
Molly Wieringa
🤔		Nicole Abib
Nicole Abib
💻 🤔		Rachel Wegener
Rachel Wegener
🐛 💻 📖 🤔 🚧 👀 ⚠️ ✅		Raphael Hagen
Raphael Hagen
📖 🎨 💻 🚇 👀		Romina Piunno
Romina Piunno
💻 🤔 🧑‍🏫 👀 ✅		Sarah Hall
Sarah Hall
🐛 💻 📖 🚧 ⚠️		Scott Henderson
Scott Henderson
🚧
Sebastian Alvis
Sebastian Alvis
📖 🚇		Shashank Bhushan
Shashank Bhushan
💡		Tian Li
Tian Li
🐛 💻 📖 💡 🤔 👀 ⚠️ 🔧		Tom Johnson
Tom Johnson
📖 🚇		Tyler Sutterley
Tyler Sutterley
📖 💻 🤔 💬 🛡️ ⚠️		Wei Ji
Wei Ji
🐛 💻 📖 💡 🤔 🚇 🚧 🧑‍🏫 💬 👀 ⚠️ 📢		Whyjay Zheng
Whyjay Zheng
✅ 🐛 💻 👀
Wilson Sauthoff
Wilson Sauthoff
👀		Zach Fair
Zach Fair
🐛 💻 📖 🤔 💬 👀 ✅		alexdibella
alexdibella
🐛 🤔 💻		bidhya
bidhya
💡		learn2phoenix
learn2phoenix
💻		liuzheng-arctic
liuzheng-arctic
📖 🐛 💻 🤔 👀 🔧 💡		nitin-ravinder
nitin-ravinder
🐛 👀
ravindraK08
ravindraK08
👀		rtilling
rtilling
🤔		smithb
smithb
🤔		tedmaksym
tedmaksym
🤔		trevorskaggs
trevorskaggs
🐛 💻		trey-stafford
trey-stafford
💻 🤔 🚧 👀 💬
- - + + - + This project follows the `all-contributors `_ specification. Contributions of any kind welcome! From a762ad88e4046678a6381fc276aed428278edd91 Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Thu, 22 Aug 2024 20:19:55 -0600 Subject: [PATCH 14/31] docs: add jrenrut as a contributor for bug, and code (#586) Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: GitHub Action --- .all-contributorsrc | 10 + CONTRIBUTORS.rst | 9 +- .../documentation/classes_dev_uml.svg | 495 +++++++++--------- .../documentation/classes_user_uml.svg | 387 +++++++------- 4 files changed, 449 insertions(+), 452 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index 715c4af76..ca0fadc4a 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -481,6 +481,16 @@ "review", "tool" ] + }, + { + "login": "jrenrut", + "name": "Jeremy Turner", + "avatar_url": "https://avatars.githubusercontent.com/u/42989238?v=4", + "profile": "https://github.com/jrenrut", + "contributions": [ + "bug", + "code" + ] } ], "contributorsPerLine": 7, diff --git a/CONTRIBUTORS.rst b/CONTRIBUTORS.rst index 04e227ce6..240447132 100644 --- a/CONTRIBUTORS.rst +++ b/CONTRIBUTORS.rst @@ -25,39 +25,40 @@ Thanks goes to these wonderful people (`emoji key Facundo Sapienza
Facundo Sapienza
💡 🐛 Fernando Perez
Fernando Perez
🎨 💼 🤔 JP Swinski
JP Swinski
💻 👀 + Jeremy Turner
Jeremy Turner
🐛 💻 Jessica
Jessica
🐛 💻 🖋 📖 🎨 💡 🤔 🚧 🧑‍🏫 📆 💬 👀 Joachim Meyer
Joachim Meyer
🧑‍🏫 🚧 Kelsey Bisson
Kelsey Bisson
🐛 💻 📖 🤔 💡 🤔 🧑‍🏫 💬 👀 ✅ - Lindsey Heagy
Lindsey Heagy
🧑‍🏫 👀 + Lindsey Heagy
Lindsey Heagy
🧑‍🏫 👀 Molly Wieringa
Molly Wieringa
🤔 Nicole Abib
Nicole Abib
💻 🤔 Rachel Wegener
Rachel Wegener
🐛 💻 📖 🤔 🚧 👀 ⚠️ ✅ Raphael Hagen
Raphael Hagen
📖 🎨 💻 🚇 👀 Romina Piunno
Romina Piunno
💻 🤔 🧑‍🏫 👀 ✅ Sarah Hall
Sarah Hall
🐛 💻 📖 🚧 ⚠️ - Scott Henderson
Scott Henderson
🚧 + Scott Henderson
Scott Henderson
🚧 Sebastian Alvis
Sebastian Alvis
📖 🚇 Shashank Bhushan
Shashank Bhushan
💡 Tian Li
Tian Li
🐛 💻 📖 💡 🤔 👀 ⚠️ 🔧 Tom Johnson
Tom Johnson
📖 🚇 Tyler Sutterley
Tyler Sutterley
📖 💻 🤔 💬 🛡️ ⚠️ Wei Ji
Wei Ji
🐛 💻 📖 💡 🤔 🚇 🚧 🧑‍🏫 💬 👀 ⚠️ 📢 - Whyjay Zheng
Whyjay Zheng
✅ 🐛 💻 👀 + Whyjay Zheng
Whyjay Zheng
✅ 🐛 💻 👀 Wilson Sauthoff
Wilson Sauthoff
👀 Zach Fair
Zach Fair
🐛 💻 📖 🤔 💬 👀 ✅ alexdibella
alexdibella
🐛 🤔 💻 bidhya
bidhya
💡 learn2phoenix
learn2phoenix
💻 liuzheng-arctic
liuzheng-arctic
📖 🐛 💻 🤔 👀 🔧 💡 - nitin-ravinder
nitin-ravinder
🐛 👀 + nitin-ravinder
nitin-ravinder
🐛 👀 ravindraK08
ravindraK08
👀 rtilling
rtilling
🤔 smithb
smithb
🤔 diff --git a/doc/source/user_guide/documentation/classes_dev_uml.svg b/doc/source/user_guide/documentation/classes_dev_uml.svg index f59739433..9084ffd70 100644 --- a/doc/source/user_guide/documentation/classes_dev_uml.svg +++ b/doc/source/user_guide/documentation/classes_dev_uml.svg @@ -4,11 +4,11 @@ - + classes_dev_uml - + icepyx.quest.dataset_scripts.argo.Argo @@ -87,316 +87,309 @@ icepyx.core.auth.EarthdataAuthMixin - -EarthdataAuthMixin - -_auth : NoneType -_s3_initial_ts : NoneType, datetime -_s3login_credentials : NoneType -_session : NoneType -auth -s3login_credentials -session - -__init__(auth) -__str__() -earthdata_login(uid, email, s3token): None + +EarthdataAuthMixin + +_auth : NoneType +_s3_initial_ts : NoneType, datetime +_s3login_credentials : NoneType +_session : NoneType +auth +s3login_credentials +session + +__init__(auth) +__str__() +earthdata_login(uid, email, s3token): None icepyx.core.query.GenQuery - -GenQuery - -_spatial -_temporal -dates -end_time -spatial -spatial_extent -start_time -temporal - -__init__(spatial_extent, date_range, start_time, end_time) -__str__() + +GenQuery + +_spatial +_temporal +dates +end_time +spatial +spatial_extent +start_time +temporal + +__init__(spatial_extent, date_range, start_time, end_time) +__str__() icepyx.core.granules.Granules - -Granules - -avail : list -orderIDs : list - -__init__() -download(verbose, path, restart) -get_avail(CMRparams, reqparams, cloud) -place_order(CMRparams, reqparams, subsetparams, verbose, subset, geom_filepath) + +Granules + +avail : list +orderIDs : list + +__init__() +download(verbose, path, restart) +get_avail(CMRparams, reqparams, cloud) +place_order(CMRparams, reqparams, subsetparams, verbose, subset, geom_filepath) icepyx.core.granules.Granules->icepyx.core.auth.EarthdataAuthMixin - - + + icepyx.core.query.Query - -Query - -CMRparams -_CMRparams -_about_product -_cust_options : dict -_cycles : list -_granules -_order_vars -_prod : NoneType, str -_readable_granule_name : list -_reqparams -_subsetparams : NoneType -_tracks : list -_version -cycles -dataset -granules -order_vars -product -product_version -reqparams -tracks - -__init__(product, spatial_extent, date_range, start_time, end_time, version, cycles, tracks, auth) -__str__() -avail_granules(ids, cycles, tracks, cloud) -download_granules(path, verbose, subset, restart) -latest_version() -order_granules(verbose, subset, email) -product_all_info() -product_summary_info() -show_custom_options(dictview) -subsetparams() -visualize_elevation() -visualize_spatial_extent() + +Query + +CMRparams +_CMRparams +_about_product +_cust_options : dict +_cycles : list +_granules +_order_vars +_prod : NoneType, str +_readable_granule_name : list +_reqparams +_subsetparams : NoneType +_tracks : list +_version +cycles +dataset +granules +order_vars +product +product_version +reqparams +tracks + +__init__(product, spatial_extent, date_range, start_time, end_time, version, cycles, tracks, auth) +__str__() +avail_granules(ids, cycles, tracks, cloud) +download_granules(path, verbose, subset, restart) +latest_version() +order_granules(verbose, subset, email) +product_all_info() +product_summary_info() +show_custom_options(dictview) +subsetparams() +visualize_elevation() +visualize_spatial_extent() icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules - - - -icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules + + +_granules icepyx.core.icesat2data.Icesat2Data - -Icesat2Data - - -__init__() + +Icesat2Data + + +__init__() icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - -__init__(errmsg, msgtxt) -__str__() + +NsidcQueryError + +errmsg +msgtxt : str + +__init__(errmsg, msgtxt) +__str__() icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + icepyx.core.APIformatting.Parameters - -Parameters - -_fmted_keys : NoneType, dict -_poss_keys : dict -_reqtype : NoneType, str -fmted_keys -partype -poss_keys - -__init__(partype, values, reqtype) -_check_valid_keys() -_get_possible_keys() -build_params() -check_req_values() -check_values() + +Parameters + +_fmted_keys : NoneType, dict +_poss_keys : dict +_reqtype : NoneType, str +fmted_keys +partype +poss_keys + +__init__(partype, values, reqtype) +_check_valid_keys() +_get_possible_keys() +build_params() +check_req_values() +check_values() icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_CMRparams + + +_CMRparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_reqparams + + +_reqparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.query.Query->icepyx.core.auth.EarthdataAuthMixin - - + + icepyx.core.query.Query->icepyx.core.query.GenQuery - - + + icepyx.quest.quest.Quest - -Quest - -datasets : dict - -__init__(spatial_extent, date_range, start_time, end_time, proj) -__str__() -add_argo(params, presRange): None -add_icesat2(product, start_time, end_time, version, cycles, tracks, files): None -download_all(path) -save_all(path) -search_all() + +Quest + +datasets : dict + +__init__(spatial_extent, date_range, start_time, end_time, proj) +__str__() +add_argo(params, presRange): None +add_icesat2(product, start_time, end_time, version, cycles, tracks, files): None +download_all(path) +save_all(path) +search_all() icepyx.quest.quest.Quest->icepyx.core.query.GenQuery - - + + icepyx.core.read.Read - -Read - -_filelist -_out_obj : Dataset -_product -_read_vars -filelist -is_s3 -product -vars - -__init__(data_source, glob_kwargs, out_obj_type, product, filename_pattern, catalog) -_add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict) -_build_dataset_template(file) -_build_single_file_dataset(file, groups_list) -_combine_nested_vars(is2ds, ds, grp_path, wanted_dict) -_read_single_grp(file, grp_path) -load() + +Read + +_filelist +_out_obj : Dataset +_product +_read_vars +filelist +is_s3 +product +vars + +__init__(data_source, glob_kwargs, out_obj_type, product, filename_pattern, catalog) +_add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict) +_build_dataset_template(file) +_build_single_file_dataset(file, groups_list) +_combine_nested_vars(is2ds, ds, grp_path, wanted_dict) +_read_single_grp(file, grp_path) +load() icepyx.core.read.Read->icepyx.core.auth.EarthdataAuthMixin - - + + icepyx.core.spatial.Spatial - -Spatial - -_ext_type : str -_gdf_spat : GeoDataFrame -_geom_file : NoneType -_spatial_ext -_xdateln -extent -extent_as_gdf -extent_file -extent_type - -__init__(spatial_extent) -__str__() -fmt_for_CMR() -fmt_for_EGI() + +Spatial + +_ext_type : str +_gdf_spat : GeoDataFrame +_geom_file : NoneType +_spatial_ext +_xdateln +extent +extent_as_gdf +extent_file +extent_type + +__init__(spatial_extent) +__str__() +fmt_for_CMR() +fmt_for_EGI() - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial icepyx.core.temporal.Temporal - -Temporal - -_end : datetime -_start : datetime -end -start - -__init__(date_range, start_time, end_time) -__str__() + +Temporal + +_end : datetime +_start : datetime +end +start + +__init__(date_range, start_time, end_time) +__str__() - + icepyx.core.temporal.Temporal->icepyx.core.query.GenQuery - - -_temporal + + +_temporal @@ -427,57 +420,57 @@ icepyx.core.variables.Variables->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars - + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : NoneType, str -tracks : NoneType - -__init__(query_obj, product, spatial_extent, date_range, cycles, tracks) -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): da.array -query_icesat2_filelist(): tuple -request_OA_data(paras): da.array -viz_elevation(): (hv.DynamicMap, hv.Layout) + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : NoneType, str +tracks : NoneType + +__init__(query_obj, product, spatial_extent, date_range, cycles, tracks) +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): da.array +query_icesat2_filelist(): tuple +request_OA_data(paras): da.array +viz_elevation(): (hv.DynamicMap, hv.Layout) diff --git a/doc/source/user_guide/documentation/classes_user_uml.svg b/doc/source/user_guide/documentation/classes_user_uml.svg index d5c17c066..8b1273598 100644 --- a/doc/source/user_guide/documentation/classes_user_uml.svg +++ b/doc/source/user_guide/documentation/classes_user_uml.svg @@ -4,11 +4,11 @@ - + classes_user_uml - + icepyx.core.auth.AuthenticationError @@ -30,313 +30,306 @@ icepyx.core.auth.EarthdataAuthMixin - -EarthdataAuthMixin - -auth -s3login_credentials -session - -earthdata_login(uid, email, s3token): None + +EarthdataAuthMixin + +auth +s3login_credentials +session + +earthdata_login(uid, email, s3token): None icepyx.core.query.GenQuery - -GenQuery - -dates -end_time -spatial -spatial_extent -start_time -temporal - - + +GenQuery + +dates +end_time +spatial +spatial_extent +start_time +temporal + + icepyx.core.granules.Granules - -Granules - -avail : list -orderIDs : list - -download(verbose, path, restart) -get_avail(CMRparams, reqparams, cloud) -place_order(CMRparams, reqparams, subsetparams, verbose, subset, geom_filepath) + +Granules + +avail : list +orderIDs : list + +download(verbose, path, restart) +get_avail(CMRparams, reqparams, cloud) +place_order(CMRparams, reqparams, subsetparams, verbose, subset, geom_filepath) icepyx.core.granules.Granules->icepyx.core.auth.EarthdataAuthMixin - - + + icepyx.core.query.Query - -Query - -CMRparams -cycles -dataset -granules -order_vars -product -product_version -reqparams -tracks - -avail_granules(ids, cycles, tracks, cloud) -download_granules(path, verbose, subset, restart) -latest_version() -order_granules(verbose, subset, email) -product_all_info() -product_summary_info() -show_custom_options(dictview) -subsetparams() -visualize_elevation() -visualize_spatial_extent() + +Query + +CMRparams +cycles +dataset +granules +order_vars +product +product_version +reqparams +tracks + +avail_granules(ids, cycles, tracks, cloud) +download_granules(path, verbose, subset, restart) +latest_version() +order_granules(verbose, subset, email) +product_all_info() +product_summary_info() +show_custom_options(dictview) +subsetparams() +visualize_elevation() +visualize_spatial_extent() icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules - - - -icepyx.core.granules.Granules->icepyx.core.query.Query - - -_granules + + +_granules icepyx.core.icesat2data.Icesat2Data - -Icesat2Data - - - + +Icesat2Data + + + icepyx.core.exceptions.NsidcQueryError - -NsidcQueryError - -errmsg -msgtxt : str - - + +NsidcQueryError + +errmsg +msgtxt : str + + icepyx.core.exceptions.QueryError - -QueryError - - - + +QueryError + + + icepyx.core.exceptions.NsidcQueryError->icepyx.core.exceptions.QueryError - - + + icepyx.core.APIformatting.Parameters - -Parameters - -fmted_keys -partype -poss_keys - -build_params() -check_req_values() -check_values() + +Parameters + +fmted_keys +partype +poss_keys + +build_params() +check_req_values() +check_values() icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_CMRparams + + +_CMRparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_reqparams + + +_reqparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.APIformatting.Parameters->icepyx.core.query.Query - - -_subsetparams + + +_subsetparams icepyx.core.query.Query->icepyx.core.auth.EarthdataAuthMixin - - + + icepyx.core.query.Query->icepyx.core.query.GenQuery - - + + icepyx.core.read.Read - -Read - -filelist -is_s3 -product -vars - -load() + +Read + +filelist +is_s3 +product +vars + +load() icepyx.core.read.Read->icepyx.core.auth.EarthdataAuthMixin - - + + icepyx.core.spatial.Spatial - -Spatial - -extent -extent_as_gdf -extent_file -extent_type - -fmt_for_CMR() -fmt_for_EGI() + +Spatial + +extent +extent_as_gdf +extent_file +extent_type + +fmt_for_CMR() +fmt_for_EGI() - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial - + icepyx.core.spatial.Spatial->icepyx.core.query.GenQuery - - -_spatial + + +_spatial icepyx.core.temporal.Temporal - -Temporal - -end -start - - + +Temporal + +end +start + + - + icepyx.core.temporal.Temporal->icepyx.core.query.GenQuery - - -_temporal + + +_temporal icepyx.core.variables.Variables - -Variables - -path -product -version -wanted : NoneType, dict - -append(defaults, var_list, beam_list, keyword_list) -avail(options, internal) -parse_var_list(varlist, tiered, tiered_vars) -remove(all, var_list, beam_list, keyword_list) + +Variables + +path +product +version +wanted : NoneType, dict + +append(defaults, var_list, beam_list, keyword_list) +avail(options, internal) +parse_var_list(varlist, tiered, tiered_vars) +remove(all, var_list, beam_list, keyword_list) icepyx.core.variables.Variables->icepyx.core.auth.EarthdataAuthMixin - - + + - + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars - + icepyx.core.variables.Variables->icepyx.core.query.Query - - -_order_vars + + +_order_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars - + icepyx.core.variables.Variables->icepyx.core.read.Read - - -_read_vars + + +_read_vars icepyx.core.visualization.Visualize - -Visualize - -bbox : list -cycles : NoneType -date_range : NoneType -product : NoneType, str -tracks : NoneType - -generate_OA_parameters(): list -grid_bbox(binsize): list -make_request(base_url, payload) -parallel_request_OA(): da.array -query_icesat2_filelist(): tuple -request_OA_data(paras): da.array -viz_elevation(): (hv.DynamicMap, hv.Layout) + +Visualize + +bbox : list +cycles : NoneType +date_range : NoneType +product : NoneType, str +tracks : NoneType + +generate_OA_parameters(): list +grid_bbox(binsize): list +make_request(base_url, payload) +parallel_request_OA(): da.array +query_icesat2_filelist(): tuple +request_OA_data(paras): da.array +viz_elevation(): (hv.DynamicMap, hv.Layout) From e491c84c12704e819d71b47a1bacd91b334743e8 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Fri, 23 Aug 2024 11:23:24 -0600 Subject: [PATCH 15/31] docs: add mfisher87 as a contributor for bug, code, and 4 more (#585) Co-authored-by: Jessica Scheick Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .all-contributorsrc | 14 +++++ CONTRIBUTORS.rst | 129 ++++++++++++++++++++++---------------------- 2 files changed, 80 insertions(+), 63 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index ca0fadc4a..bfdbf3cc6 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -491,6 +491,20 @@ "bug", "code" ] + }, + { + "login": "mfisher87", + "name": "Matt Fisher", + "avatar_url": "https://avatars.githubusercontent.com/u/3608264?v=4", + "profile": "https://mfisher87.github.io/", + "contributions": [ + "bug", + "code", + "doc", + "maintenance", + "test", + "infra" + ] } ], "contributorsPerLine": 7, diff --git a/CONTRIBUTORS.rst b/CONTRIBUTORS.rst index 240447132..aeea99573 100644 --- a/CONTRIBUTORS.rst +++ b/CONTRIBUTORS.rst @@ -8,70 +8,73 @@ Thanks goes to these wonderful people (`emoji key - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Amy Steiker
Amy Steiker
💡 📖 🧑‍🏫		Anna Valentine
Anna Valentine
💡		Anthony Arendt
Anthony Arendt
🐛 💼 📋 🔍		Bruce Wallin
Bruce Wallin
💻 📖 🤔 👀 💬		Christian Clauss
Christian Clauss
🚧 👀 🔧		David Shean
David Shean
🐛 🧑‍🏫		Don Setiawan
Don Setiawan
🚇 📦
Facundo Sapienza
Facundo Sapienza
💡 🐛		Fernando Perez
Fernando Perez
🎨 💼 🤔		JP Swinski
JP Swinski
💻 👀		Jeremy Turner
Jeremy Turner
🐛 💻		Jessica
Jessica
🐛 💻 🖋 📖 🎨 💡 🤔 🚧 🧑‍🏫 📆 💬 👀		Joachim Meyer
Joachim Meyer
🧑‍🏫 🚧		Kelsey Bisson
Kelsey Bisson
🐛 💻 📖 🤔 💡 🤔 🧑‍🏫 💬 👀 ✅
Lindsey Heagy
Lindsey Heagy
🧑‍🏫 👀		Molly Wieringa
Molly Wieringa
🤔		Nicole Abib
Nicole Abib
💻 🤔		Rachel Wegener
Rachel Wegener
🐛 💻 📖 🤔 🚧 👀 ⚠️ ✅		Raphael Hagen
Raphael Hagen
📖 🎨 💻 🚇 👀		Romina Piunno
Romina Piunno
💻 🤔 🧑‍🏫 👀 ✅		Sarah Hall
Sarah Hall
🐛 💻 📖 🚧 ⚠️
Scott Henderson
Scott Henderson
🚧		Sebastian Alvis
Sebastian Alvis
📖 🚇		Shashank Bhushan
Shashank Bhushan
💡		Tian Li
Tian Li
🐛 💻 📖 💡 🤔 👀 ⚠️ 🔧		Tom Johnson
Tom Johnson
📖 🚇		Tyler Sutterley
Tyler Sutterley
📖 💻 🤔 💬 🛡️ ⚠️		Wei Ji
Wei Ji
🐛 💻 📖 💡 🤔 🚇 🚧 🧑‍🏫 💬 👀 ⚠️ 📢
Whyjay Zheng
Whyjay Zheng
✅ 🐛 💻 👀		Wilson Sauthoff
Wilson Sauthoff
👀		Zach Fair
Zach Fair
🐛 💻 📖 🤔 💬 👀 ✅		alexdibella
alexdibella
🐛 🤔 💻		bidhya
bidhya
💡		learn2phoenix
learn2phoenix
💻		liuzheng-arctic
liuzheng-arctic
📖 🐛 💻 🤔 👀 🔧 💡
nitin-ravinder
nitin-ravinder
🐛 👀		ravindraK08
ravindraK08
👀		rtilling
rtilling
🤔		smithb
smithb
🤔		tedmaksym
tedmaksym
🤔		trevorskaggs
trevorskaggs
🐛 💻		trey-stafford
trey-stafford
💻 🤔 🚧 👀 💬
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Amy Steiker
Amy Steiker
💡 📖 🧑‍🏫		Anna Valentine
Anna Valentine
💡		Anthony Arendt
Anthony Arendt
🐛 💼 📋 🔍		Bruce Wallin
Bruce Wallin
💻 📖 🤔 👀 💬		Christian Clauss
Christian Clauss
🚧 👀 🔧		David Shean
David Shean
🐛 🧑‍🏫		Don Setiawan
Don Setiawan
🚇 📦
Facundo Sapienza
Facundo Sapienza
💡 🐛		Fernando Perez
Fernando Perez
🎨 💼 🤔		JP Swinski
JP Swinski
💻 👀		Jeremy Turner
Jeremy Turner
🐛 💻		Jessica
Jessica
🐛 💻 🖋 📖 🎨 💡 🤔 🚧 🧑‍🏫 📆 💬 👀		Joachim Meyer
Joachim Meyer
🧑‍🏫 🚧		Kelsey Bisson
Kelsey Bisson
🐛 💻 📖 🤔 💡 🤔 🧑‍🏫 💬 👀 ✅
Lindsey Heagy
Lindsey Heagy
🧑‍🏫 👀		Matt Fisher
Matt Fisher
🐛 💻 📖 🚧 ⚠️ 🚇		Molly Wieringa
Molly Wieringa
🤔		Nicole Abib
Nicole Abib
💻 🤔		Rachel Wegener
Rachel Wegener
🐛 💻 📖 🤔 🚧 👀 ⚠️ ✅		Raphael Hagen
Raphael Hagen
📖 🎨 💻 🚇 👀		Romina Piunno
Romina Piunno
💻 🤔 🧑‍🏫 👀 ✅
Sarah Hall
Sarah Hall
🐛 💻 📖 🚧 ⚠️		Scott Henderson
Scott Henderson
🚧		Sebastian Alvis
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📖 🚇		Shashank Bhushan
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💡		Tian Li
Tian Li
🐛 💻 📖 💡 🤔 👀 ⚠️ 🔧		Tom Johnson
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📖 🚇		Tyler Sutterley
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Wei Ji
Wei Ji
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Whyjay Zheng
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👀		Zach Fair
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🐛 💻 📖 🤔 💬 👀 ✅		alexdibella
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🐛 👀		ravindraK08
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👀		rtilling
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- - + + - + This project follows the `all-contributors `_ specification. Contributions of any kind welcome! From 2790edd15a9112d0a9d6df04b4705654669440c3 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Mon, 26 Aug 2024 13:37:48 -0600 Subject: [PATCH 16/31] Tweak format and wording of contributor doc (#566) Co-authored-by: Jessica Scheick --- doc/source/contributing/how_to_contribute.rst | 64 +++++++++++-------- 1 file changed, 36 insertions(+), 28 deletions(-) diff --git a/doc/source/contributing/how_to_contribute.rst b/doc/source/contributing/how_to_contribute.rst index 84c21717b..3211c0947 100644 --- a/doc/source/contributing/how_to_contribute.rst +++ b/doc/source/contributing/how_to_contribute.rst @@ -3,9 +3,9 @@ How to Contribute ================= -On this page we briefly provide basic instructions for contributing to icepyx. +On this page we provide brief instructions for contributing to icepyx. We encourage users to follow the `git pull request workflow `_. -For contribution examples, please see contribution guidelines. +For contribution examples, please see :doc:`contribution guidelines `. Contributing for the first time @@ -13,52 +13,60 @@ Contributing for the first time 1. If you don't have one, sign up for a GitHub account (visit https://github.com/ and ‘sign up for GitHub account’). 2. Clone the icepyx repo: Open a terminal window. -Navigate to the folder on your computer where you want to store icepyx. -For example, + Navigate to the folder on your computer where you want to store icepyx. + For example, -.. code-block:: shell + .. code-block:: shell - cd /Users/YOURNAMEHERE/documents/ICESat-2 + cd /Users/YOURNAMEHERE/documents/ICESat-2 -Within this folder, clone the icepyx repo by executing + Within this folder, clone the icepyx repo by executing -.. code-block:: shell + .. code-block:: shell - git clone https://github.com/icesat2py/icepyx.git + git clone https://github.com/icesat2py/icepyx.git -You should receive confirmation in terminal of the files loading into your workspace. -For help navigating git and GitHub, see this `guide `__. -`GitHub `_ also provides a lot of great how-to materials for navigating and contributing. +You should receive confirmation in terminal of the files downloading into your workspace. +For help navigating ``git`` and GitHub, see this `guide `__. +`GitHub `_ also provides great how-to materials for navigating and contributing. Every time you contribute ------------------------- +.. important:: + + If you do not have write permissions on this repository, start with creating a fork by clicking the Fork button in GitHub. + All actions from here on should be performed in your fork. + 1. To add new content, you need to create a new branch. -You can do this on GitHub by clicking the down arrow next to ‘development’ and making a new branch -(you can give it whatever name you want - the naming doesn't matter much as it will only be a temporary branch). + You can do this on GitHub by clicking the down arrow next to ‘development’ and making a new branch + (you can give it whatever name you want - the naming doesn't matter much as it will only be a temporary branch). 2. Navigate to the new branch you created. -Make any edits or additions on this branch (this can be done locally or on GitHub directly). -After you do this, commit your changes and add a descriptive commit message. + Make any edits or additions on this branch (this can be done locally with ``git`` or on GitHub directly). + After you do this, commit your changes and add a descriptive commit message. -3. After committing the changes, push them to GitHub if you were working locally. -Then, open a pull request to merge your branch into the development branch. -Members of the icepyx community will review your changes and may ask you to make some more. +3. Push your new commits to GitHub if you were working locally. + Then, open a pull request to merge your branch into the ``development`` branch. + Members of the icepyx community will review your changes and may ask you to make some more. 4. If this is your first PR, someone on the icepyx team should add you to the contributors list. -icepyx follows the `all-contributors `_ specification using the contributors bot to add new contributors. -You are also welcome to add yourself by adding a comment with the text: + icepyx follows the `all-contributors `_ specification using the contributors bot to add new contributors. + You are also welcome to add yourself by adding a comment with the text: -.. code-block:: none + .. code-block:: none - @all-contributors add @[GitHub_handle] for a, b, and c + @all-contributors add @[GitHub_handle] for a, b, and c -where a, b, etc. is a list of the appropriate `contribution emojis `_. -The bot will open a separate PR to add the contributor or new contribution types! + where a, b, etc. is a list of the appropriate `contribution emojis `_. + The bot will open a separate PR to add the contributor or new contribution types! 5. Repeat these steps, creating a new branch and ultimately a pull request for each change. -More, smaller pull requests are easier to debug and merge than fewer large ones, so create pull requests regularly! + + .. tip:: + + More, smaller pull requests are easier to debug and merge than fewer large ones, so please create pull requests regularly! Steps for working with icepyx locally @@ -94,10 +102,10 @@ environment (from the home level of your local copy of the icepyx repo) with mamba env create --name icepyx-env --channel conda-forge -f requirements-dev.txt -f requirements.txt -and then (1) running `pre-commit install` to let git know about pre-commit and +and then (1) running ``pre-commit install`` to let git know about pre-commit and (2) pip installing icepyx as described above and below. -One of the tools installed with "requirements-dev.txt" is called [pre-commit](https://pre-commit.com/). +One of the tools installed with "requirements-dev.txt" is called `pre-commit `_. We have included a set of pre-commit formatting hooks that we strongly encourage all contributors to use. These hooks will check the files you are committing for format consistency, reformatting the files if necessary. From ee4346193dc0cb94835cf583dea7efbeb0914979 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 27 Aug 2024 13:42:29 -0600 Subject: [PATCH 17/31] More ruff & pre-commit rules (#546) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> --- .pre-commit-config.yaml | 8 +++++++ doc/source/conf.py | 4 +--- .../tracking/pypistats/get_pypi_stats.py | 3 ++- .../tracking/traffic/traffic_data_mgmt.py | 3 ++- doc/sphinxext/announce.py | 0 icepyx/__init__.py | 8 +++---- icepyx/conftest.py | 3 ++- icepyx/core/APIformatting.py | 1 - icepyx/core/auth.py | 3 +-- icepyx/core/exceptions.py | 4 ---- icepyx/core/granules.py | 9 +++---- icepyx/core/is2ref.py | 7 +++--- icepyx/core/query.py | 5 ++-- icepyx/core/read.py | 4 ++-- icepyx/core/spatial.py | 8 +++---- icepyx/core/temporal.py | 1 - icepyx/core/validate_inputs.py | 1 + icepyx/core/variables.py | 5 ++-- icepyx/core/visualization.py | 4 ++-- icepyx/quest/quest.py | 1 - icepyx/tests/conftest.py | 3 ++- icepyx/tests/test_APIformatting.py | 1 - icepyx/tests/test_Earthdata.py | 4 ++-- icepyx/tests/test_auth.py | 3 +-- icepyx/tests/test_behind_NSIDC_API_login.py | 2 +- icepyx/tests/test_granules.py | 5 ++-- ...2class_query.py => test_is2class_query.py} | 6 +++++ icepyx/tests/test_quest_argo.py | 2 +- icepyx/tests/test_read.py | 9 +++---- icepyx/tests/test_spatial.py | 6 ++--- icepyx/tests/test_temporal.py | 2 +- pyproject.toml | 24 +++++++++++++++++++ 32 files changed, 92 insertions(+), 57 deletions(-) mode change 100644 => 100755 doc/sphinxext/announce.py rename icepyx/tests/{is2class_query.py => test_is2class_query.py} (86%) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index dc1236159..934cdbb97 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,9 +6,17 @@ repos: - id: check-yaml - id: check-added-large-files args: ["--maxkb=5000"] + - id: check-case-conflict + - id: check-merge-conflict + - id: check-symlinks + - id: debug-statements + - id: name-tests-test + args: ["--pytest-test-first"] - id: end-of-file-fixer + - id: mixed-line-ending - id: trailing-whitespace args: [--markdown-linebreak-ext=md] + - id: requirements-txt-fixer - repo: https://github.com/codespell-project/codespell rev: v2.3.0 diff --git a/doc/source/conf.py b/doc/source/conf.py index 868af3fbc..0303f72ca 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -19,7 +19,6 @@ import icepyx - # -- Project information ----------------------------------------------------- project = "icepyx" @@ -120,10 +119,9 @@ def setup(app): # this should possibly be moved to the sphinxext directory as a standalone .py file # -- custom style for pybtex output ------------------------------------------- -from pybtex.style.formatting.unsrt import Style as UnsrtStyle - # from pybtex.style.labels.alpha import LabelStyle as AlphaLabelStyle from pybtex.plugin import register_plugin +from pybtex.style.formatting.unsrt import Style as UnsrtStyle # I seem to be unable to figure out how to control what is used for the label. It would # make sense if it were fed into this function, which then just formatted it, but I can't figure out from where diff --git a/doc/source/tracking/pypistats/get_pypi_stats.py b/doc/source/tracking/pypistats/get_pypi_stats.py index d137b99c3..78a197e8f 100644 --- a/doc/source/tracking/pypistats/get_pypi_stats.py +++ b/doc/source/tracking/pypistats/get_pypi_stats.py @@ -1,6 +1,7 @@ import os -import pypistats + import pandas as pd +import pypistats cwd = os.getcwd() diff --git a/doc/source/tracking/traffic/traffic_data_mgmt.py b/doc/source/tracking/traffic/traffic_data_mgmt.py index 0d0a6af9c..5cdf0672b 100644 --- a/doc/source/tracking/traffic/traffic_data_mgmt.py +++ b/doc/source/tracking/traffic/traffic_data_mgmt.py @@ -1,5 +1,6 @@ -import matplotlib.pyplot as plt import os + +import matplotlib.pyplot as plt import pandas as pd cwd = os.getcwd() diff --git a/doc/sphinxext/announce.py b/doc/sphinxext/announce.py old mode 100644 new mode 100755 diff --git a/icepyx/__init__.py b/icepyx/__init__.py index 40ea9e1ec..a9d61834b 100644 --- a/icepyx/__init__.py +++ b/icepyx/__init__.py @@ -1,6 +1,6 @@ -from icepyx.core.query import Query, GenQuery +from _icepyx_version import version as __version__ + +from icepyx.core.query import GenQuery, Query from icepyx.core.read import Read -from icepyx.quest.quest import Quest from icepyx.core.variables import Variables - -from _icepyx_version import version as __version__ +from icepyx.quest.quest import Quest diff --git a/icepyx/conftest.py b/icepyx/conftest.py index d90558d69..a8bae49c4 100644 --- a/icepyx/conftest.py +++ b/icepyx/conftest.py @@ -1,6 +1,7 @@ -import icepyx import pytest +import icepyx + @pytest.fixture(autouse=True) def add_ipx(doctest_namespace): diff --git a/icepyx/core/APIformatting.py b/icepyx/core/APIformatting.py index 90b7f3ac6..8761a8343 100644 --- a/icepyx/core/APIformatting.py +++ b/icepyx/core/APIformatting.py @@ -2,7 +2,6 @@ import datetime as dt - # ---------------------------------------------------------------------- # parameter-specific formatting for display # or input to a set of API parameters (CMR or NSIDC) diff --git a/icepyx/core/auth.py b/icepyx/core/auth.py index 8e263e730..9f12fbecf 100644 --- a/icepyx/core/auth.py +++ b/icepyx/core/auth.py @@ -2,6 +2,7 @@ import datetime import earthaccess + from icepyx.core.exceptions import DeprecationError @@ -10,8 +11,6 @@ class AuthenticationError(Exception): Raised when an error is encountered while authenticating Earthdata credentials """ - pass - class EarthdataAuthMixin: """ diff --git a/icepyx/core/exceptions.py b/icepyx/core/exceptions.py index d20bbfe61..94bbea768 100644 --- a/icepyx/core/exceptions.py +++ b/icepyx/core/exceptions.py @@ -3,16 +3,12 @@ class DeprecationError(Exception): Class raised for use of functionality that is no longer supported by icepyx. """ - pass - class QueryError(Exception): """ Base class for Query object exceptions """ - pass - class NsidcQueryError(QueryError): """ diff --git a/icepyx/core/granules.py b/icepyx/core/granules.py index 2c51e208b..7c748fe6f 100644 --- a/icepyx/core/granules.py +++ b/icepyx/core/granules.py @@ -1,15 +1,16 @@ import datetime -import requests -import time import io -import re import json -import numpy as np import os import pprint +import re +import time from xml.etree import ElementTree as ET import zipfile +import numpy as np +import requests + import icepyx.core.APIformatting as apifmt from icepyx.core.auth import EarthdataAuthMixin import icepyx.core.exceptions diff --git a/icepyx/core/is2ref.py b/icepyx/core/is2ref.py index be3a3c8da..1cd58f10a 100644 --- a/icepyx/core/is2ref.py +++ b/icepyx/core/is2ref.py @@ -1,12 +1,11 @@ -import h5py import json -import numpy as np -import requests import warnings from xml.etree import ElementTree as ET import earthaccess - +import h5py +import numpy as np +import requests # ICESat-2 specific reference functions diff --git a/icepyx/core/query.py b/icepyx/core/query.py index ed241662b..d547a959f 100644 --- a/icepyx/core/query.py +++ b/icepyx/core/query.py @@ -1,6 +1,7 @@ +import pprint + import geopandas as gpd import matplotlib.pyplot as plt -import pprint import icepyx.core.APIformatting as apifmt from icepyx.core.auth import EarthdataAuthMixin @@ -1131,8 +1132,8 @@ def visualize_spatial_extent( gdf = self._spatial.extent_as_gdf try: - from shapely.geometry import Polygon # noqa: F401 import geoviews as gv + from shapely.geometry import Polygon # noqa: F401 gv.extension("bokeh") diff --git a/icepyx/core/read.py b/icepyx/core/read.py index 28da685d7..b3212aef2 100644 --- a/icepyx/core/read.py +++ b/icepyx/core/read.py @@ -432,7 +432,7 @@ def _add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict): ] # handle delta_times with 1 or more dimensions - idx_range = range(0, len(ds.delta_time.data)) + idx_range = range(len(ds.delta_time.data)) try: photon_ids = ( idx_range @@ -440,7 +440,7 @@ def _add_vars_to_ds(is2ds, ds, grp_path, wanted_groups_tiered, wanted_dict): + 1 ) except AttributeError: - photon_ids = range(0, len(ds.delta_time.data)) + photon_ids = range(len(ds.delta_time.data)) hold_delta_times = ds.delta_time.data ds = ( diff --git a/icepyx/core/spatial.py b/icepyx/core/spatial.py index 650ca06be..0bc066e78 100644 --- a/icepyx/core/spatial.py +++ b/icepyx/core/spatial.py @@ -1,10 +1,10 @@ -import geopandas as gpd -import numpy as np import os -from shapely.geometry import box, Polygon -from shapely.geometry.polygon import orient import warnings +import geopandas as gpd +import numpy as np +from shapely.geometry import Polygon, box +from shapely.geometry.polygon import orient # DevGoal: need to update the spatial_extent docstring to describe coordinate order for input diff --git a/icepyx/core/temporal.py b/icepyx/core/temporal.py index 67f59882a..c02326fbf 100644 --- a/icepyx/core/temporal.py +++ b/icepyx/core/temporal.py @@ -1,7 +1,6 @@ import datetime as dt import warnings - """ Helper functions for validation of dates """ diff --git a/icepyx/core/validate_inputs.py b/icepyx/core/validate_inputs.py index e70a8f944..db5e44d05 100644 --- a/icepyx/core/validate_inputs.py +++ b/icepyx/core/validate_inputs.py @@ -1,5 +1,6 @@ import datetime as dt import warnings + import numpy as np diff --git a/icepyx/core/variables.py b/icepyx/core/variables.py index bf4a38c66..b7b1c56b8 100644 --- a/icepyx/core/variables.py +++ b/icepyx/core/variables.py @@ -1,9 +1,10 @@ -import numpy as np import os +import numpy as np + from icepyx.core.auth import EarthdataAuthMixin -import icepyx.core.is2ref as is2ref from icepyx.core.exceptions import DeprecationError +import icepyx.core.is2ref as is2ref import icepyx.core.validate_inputs as val # DEVGOAL: use h5py to simplify some of these tasks, if possible! diff --git a/icepyx/core/visualization.py b/icepyx/core/visualization.py index 5df884e2d..0ddb9fd40 100644 --- a/icepyx/core/visualization.py +++ b/icepyx/core/visualization.py @@ -10,15 +10,15 @@ import dask.dataframe as dd import datashader as ds import holoviews as hv +from holoviews.operation.datashader import rasterize import numpy as np import pandas as pd import requests -from holoviews.operation.datashader import rasterize from tqdm import tqdm import icepyx as ipx -import icepyx.core.is2ref as is2ref import icepyx.core.granules as granules +import icepyx.core.is2ref as is2ref hv.extension("bokeh") diff --git a/icepyx/quest/quest.py b/icepyx/quest/quest.py index b61376625..c24029070 100644 --- a/icepyx/quest/quest.py +++ b/icepyx/quest/quest.py @@ -1,5 +1,4 @@ from icepyx.core.query import GenQuery, Query - from icepyx.quest.dataset_scripts.argo import Argo diff --git a/icepyx/tests/conftest.py b/icepyx/tests/conftest.py index 9ce8e4081..5bc5eb870 100644 --- a/icepyx/tests/conftest.py +++ b/icepyx/tests/conftest.py @@ -1,7 +1,8 @@ import os -import pytest from unittest import mock +import pytest + # PURPOSE: mock environmental variables @pytest.fixture(scope="session", autouse=True) diff --git a/icepyx/tests/test_APIformatting.py b/icepyx/tests/test_APIformatting.py index 6dfe98353..0c7009d10 100644 --- a/icepyx/tests/test_APIformatting.py +++ b/icepyx/tests/test_APIformatting.py @@ -2,7 +2,6 @@ import icepyx.core.APIformatting as apifmt - # DevNote: is this a situation where you'd ideally build a test class, # since you're just repeating the test function with different inputs? # Especially for the _fmt_spaital, where there's >2 tests? diff --git a/icepyx/tests/test_Earthdata.py b/icepyx/tests/test_Earthdata.py index 06b0bc150..403159e04 100644 --- a/icepyx/tests/test_Earthdata.py +++ b/icepyx/tests/test_Earthdata.py @@ -1,13 +1,13 @@ -#!/usr/bin/env python """ test icepyx.core.query.Query.earthdata_login function """ import netrc import os -import pytest import shutil +import pytest + # PURPOSE: test different authentication methods @pytest.fixture(scope="module", autouse=True) diff --git a/icepyx/tests/test_auth.py b/icepyx/tests/test_auth.py index 9b720a0f8..97d40344d 100644 --- a/icepyx/tests/test_auth.py +++ b/icepyx/tests/test_auth.py @@ -1,8 +1,7 @@ +import earthaccess import pytest import requests -import earthaccess - from icepyx.core.auth import EarthdataAuthMixin diff --git a/icepyx/tests/test_behind_NSIDC_API_login.py b/icepyx/tests/test_behind_NSIDC_API_login.py index bf77da074..b3824030e 100644 --- a/icepyx/tests/test_behind_NSIDC_API_login.py +++ b/icepyx/tests/test_behind_NSIDC_API_login.py @@ -1,11 +1,11 @@ import json import os + import pytest import icepyx as ipx import icepyx.core.is2ref as is2ref - # Misc notes and needed tests # test avail data and subsetting success for each input type # (kml, shp, list of coords, bbox) diff --git a/icepyx/tests/test_granules.py b/icepyx/tests/test_granules.py index 8b00ce91d..90e3374d9 100644 --- a/icepyx/tests/test_granules.py +++ b/icepyx/tests/test_granules.py @@ -1,11 +1,12 @@ -import pytest import re + +import pytest import responses import icepyx as ipx from icepyx.core import granules as granules -from icepyx.core.granules import Granules as Granules from icepyx.core.exceptions import NsidcQueryError +from icepyx.core.granules import Granules as Granules # @pytest.fixture # def reg_a(): diff --git a/icepyx/tests/is2class_query.py b/icepyx/tests/test_is2class_query.py similarity index 86% rename from icepyx/tests/is2class_query.py rename to icepyx/tests/test_is2class_query.py index 84c31cfa4..b05e0f654 100644 --- a/icepyx/tests/is2class_query.py +++ b/icepyx/tests/test_is2class_query.py @@ -1,5 +1,11 @@ +import pytest + import icepyx as ipx +# Skip the whole module. See: +# https://docs.pytest.org/en/stable/reference/reference.html#globalvar-pytestmark +pytestmark = pytest.mark.skip("Legacy tests -- not sure if they ever passed!") + def test_CMRparams(): reg_a = ipx.Query("ATL06", [-64, 66, -55, 72], ["2019-02-22", "2019-02-28"]) diff --git a/icepyx/tests/test_quest_argo.py b/icepyx/tests/test_quest_argo.py index f2c677e8d..e11e0cbe1 100644 --- a/icepyx/tests/test_quest_argo.py +++ b/icepyx/tests/test_quest_argo.py @@ -1,7 +1,7 @@ import os +import re import pytest -import re from icepyx.quest.quest import Quest diff --git a/icepyx/tests/test_read.py b/icepyx/tests/test_read.py index 20807c410..90efe13f9 100644 --- a/icepyx/tests/test_read.py +++ b/icepyx/tests/test_read.py @@ -29,12 +29,12 @@ def test_parse_source_no_files(): ( # check list input [ "./icepyx/core/is2ref.py", - "./icepyx/tests/is2class_query.py", + "./icepyx/tests/test_is2class_query.py", ], sorted( [ "./icepyx/core/is2ref.py", - "./icepyx/tests/is2class_query.py", + "./icepyx/tests/test_is2class_query.py", ] ), ), @@ -45,11 +45,12 @@ def test_parse_source_no_files(): ], ), ( # check filename string with glob pattern input - "./icepyx/**/is2*.py", + "./icepyx/**/*is2*.py", sorted( [ "./icepyx/core/is2ref.py", - "./icepyx/tests/is2class_query.py", + "./icepyx/tests/test_is2class_query.py", + "./icepyx/tests/test_is2ref.py", ] ), ), diff --git a/icepyx/tests/test_spatial.py b/icepyx/tests/test_spatial.py index dc71cdac9..2243c0674 100644 --- a/icepyx/tests/test_spatial.py +++ b/icepyx/tests/test_spatial.py @@ -1,13 +1,13 @@ +from pathlib import Path +import re + import geopandas as gpd import numpy as np -from pathlib import Path import pytest -import re from shapely.geometry import Polygon import icepyx.core.spatial as spat - # ######### "Bounding Box" input tests ################################################################################ # (Note that these ALSO test the @property functions for the class for bounding boxes) diff --git a/icepyx/tests/test_temporal.py b/icepyx/tests/test_temporal.py index cd24deda4..52ec947c3 100644 --- a/icepyx/tests/test_temporal.py +++ b/icepyx/tests/test_temporal.py @@ -1,9 +1,9 @@ import datetime as dt + import pytest import icepyx.core.temporal as tp - # DevNote: this test suite needs to be parameterized (and fixtured) to include ALL acceptable input types # Currently it tests most cases for lists and dicts where the input type is str # A couple of tests were added for datetime.datetime type inputs, but they are incomplete diff --git a/pyproject.toml b/pyproject.toml index 66eb7b6f9..e1ea8ed90 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -73,12 +73,33 @@ extend-exclude = ["*.ipynb"] # docstring-code-format = true # docstring-code-line-length = "dynamic" + [tool.ruff.lint] +# DevGoal: Enable "ARG" and "B" rulesets ASAP! select = [ + # "ARG", # flake8-unused-arguments + # "B", # flake8-bugbear "C4", # flake8-comprehensions "E", # pycodestyle + # "EM", # flake8-errmsg + "EXE", # flake8-executable "F", # pyflakes + "G", # flake8-logging-format + "I", # isort + "ICN", # flake8-import-conventions + "NPY", # NumPy specific rules + # "PD", # pandas-vet + "PGH", # pygrep-hooks + "PIE", # flake8-pie + # "PL", # pylint + # "PT", # flake8-pytest-style + # "PTH", # flake8-use-pathlib + # "RET", # flake8-return + # "RUF", # Ruff-specific "SIM", # flake8-simplify + # "T20", # flake8-print + # "UP", # pyupgrade + "YTT", # flake8-2020 ] ignore = [ # Line too long @@ -102,3 +123,6 @@ ignore = [ # Ignore too many leading '#' for block comment "*/tests/*" = ["E266"] + +[tool.ruff.lint.isort] +force-sort-within-sections = true From 50f9351c75579b33bb085d90a5ee750e49a1b7d9 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 27 Aug 2024 14:25:33 -0600 Subject: [PATCH 18/31] Fix minor typo (#589) --- icepyx/core/APIformatting.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/icepyx/core/APIformatting.py b/icepyx/core/APIformatting.py index 8761a8343..f30f9a11c 100644 --- a/icepyx/core/APIformatting.py +++ b/icepyx/core/APIformatting.py @@ -208,7 +208,7 @@ def __init__(self, partype, values=None, reqtype=None): "CMR", "required", "subset", - ], "You need to submit a valid parametery type." + ], "You need to submit a valid parameter type." self.partype = partype if partype == "required": From a52bc378ab5817db38cd2b47b5ab0c5352128061 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 27 Aug 2024 14:33:06 -0600 Subject: [PATCH 19/31] Clarify some comments / docstrings (#592) --- icepyx/core/APIformatting.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/icepyx/core/APIformatting.py b/icepyx/core/APIformatting.py index f30f9a11c..4b1966910 100644 --- a/icepyx/core/APIformatting.py +++ b/icepyx/core/APIformatting.py @@ -121,6 +121,9 @@ def combine_params(*param_dicts): """ Combine multiple dictionaries into one. + Merging is performed in sequence using `dict.update()`; dictionaries later in the + list overwrite those earlier. + Parameters ---------- params : dictionaries @@ -128,7 +131,7 @@ def combine_params(*param_dicts): Returns ------- - single dictionary of all input dictionaries combined + A single dictionary of all input dictionaries combined Examples -------- @@ -410,7 +413,10 @@ def build_params(self, **kwargs): for key in opt_keys: if key == "Coverage" and key in kwargs: - # DevGoal: make there be an option along the lines of Coverage=default, which will get the default variables for that product without the user having to input is2obj.build_wanted_wanted_var_list as their input value for using the Coverage kwarg + # DevGoal: make an option along the lines of Coverage=default, + # which will get the default variables for that product without + # the user having to input is2obj.build_wanted_wanted_var_list + # as their input value for using the Coverage kwarg self._fmted_keys.update( {key: _fmt_var_subset_list(kwargs[key])} ) From bd09d73b014f43dfa9dd5254d9b08f414e6792c4 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Wed, 28 Aug 2024 19:26:09 -0600 Subject: [PATCH 20/31] Migrate unit and integration tests from TravisCI to GitHub Actions (#580) Co-authored-by: Jessica Scheick Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- .github/actions/install-icepyx/action.yml | 19 ++++++++ .github/workflows/integration_test.yml | 53 +++++++++++++++++++++++ .github/workflows/unit_test.yml | 40 +++++++++++++++++ .travis.yml | 44 ------------------- README.rst | 18 +++++--- 5 files changed, 124 insertions(+), 50 deletions(-) create mode 100644 .github/actions/install-icepyx/action.yml create mode 100644 .github/workflows/integration_test.yml create mode 100644 .github/workflows/unit_test.yml delete mode 100644 .travis.yml diff --git a/.github/actions/install-icepyx/action.yml b/.github/actions/install-icepyx/action.yml new file mode 100644 index 000000000..fb738d7cd --- /dev/null +++ b/.github/actions/install-icepyx/action.yml @@ -0,0 +1,19 @@ +name: 'Install icepyx' +description: 'Install icepyx and dev dependencies' + +inputs: + python-version: + required: true + +runs: + using: "composite" + steps: + - uses: "actions/setup-python@v5" + with: + python-version: "${{ inputs.python-version }}" + + - name: "Install package and test dependencies" + shell: "bash" + run: | + python -m pip install . + python -m pip install -r requirements-dev.txt diff --git a/.github/workflows/integration_test.yml b/.github/workflows/integration_test.yml new file mode 100644 index 000000000..1c9dc6ed7 --- /dev/null +++ b/.github/workflows/integration_test.yml @@ -0,0 +1,53 @@ +name: "Integration test" +# NOTE: We're just running the tests that require earthdata login here; we +# don't distinguish between unit and integration tests yet. + +on: + push: + branches: + - "main" # Releases + - "development" # PR merges + pull_request: + branches: + - "main" # Release pull requests + pull_request_review: + types: + - "submitted" + paths: + - ".github/**" + - "icepyx/**/*.py" + - "pyproject.toml" + - "requirements*.txt" + + +jobs: + test: + name: "Integration test" + # Job is conditional: + # - Do not run on PRs from forks + # - Do not run on `pull_request_review` events unless the PR is approved. + if: "${{ !github.event.pull_request.head.repo.fork && (github.event.action != 'pull_request_review' || github.event.review.state == 'approved') }}" + runs-on: "ubuntu-latest" + + steps: + - uses: "actions/checkout@v4" + with: + fetch-depth: 0 + + - uses: "./.github/actions/install-icepyx" + with: + python-version: "3.12" + + - name: "Run tests" + env: + EARTHDATA_PASSWORD: "${{ secrets.EARTHDATA_PASSWORD }}" + NSIDC_LOGIN: "${{ secrets.EARTHDATA_PASSWORD }}" + run: | + pytest icepyx/ --verbose --cov app \ + icepyx/tests/test_behind_NSIDC_API_login.py \ + icepyx/tests/test_auth.py + + - name: "Upload coverage report" + uses: "codecov/codecov-action@v4.5.0" + with: + token: "${{ secrets.CODECOV_TOKEN }}" diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml new file mode 100644 index 000000000..989c7e298 --- /dev/null +++ b/.github/workflows/unit_test.yml @@ -0,0 +1,40 @@ +name: "Unit test" +# NOTE: We're just skipping the tests requiring earthdata login here; we don't +# distinguish yet between unit and integration tests. + +on: + pull_request: + push: + branches: + - "main" + - "development" + + +jobs: + test: + name: "Unit test (Python ${{ matrix.python-version }})" + runs-on: "ubuntu-latest" + strategy: + fail-fast: false + matrix: + python-version: ["3.9", "3.12"] #NOTE: min and max Python versions supported by icepyx + + steps: + - uses: "actions/checkout@v4" + with: + fetch-depth: 0 + + - uses: "./.github/actions/install-icepyx" + with: + python-version: "${{ matrix.python-version }}" + + - name: "Run tests" + run: | + pytest icepyx/ --verbose --cov app \ + --ignore=icepyx/tests/test_behind_NSIDC_API_login.py \ + --ignore=icepyx/tests/test_auth.py + + - name: "Upload coverage report" + uses: "codecov/codecov-action@v4.5.0" + with: + token: "${{ secrets.CODECOV_TOKEN }}" diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 271eb5bff..000000000 --- a/.travis.yml +++ /dev/null @@ -1,44 +0,0 @@ -language: python - -before_install: - - sudo apt-get update - - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh - - bash miniconda.sh -b -p $HOME/miniconda - - export PATH="$HOME/miniconda/bin:$PATH" - - hash -r - - conda config --set always_yes yes --set changeps1 no - - conda update -q conda - # Useful for debugging any issues with conda - - conda info -a - -install: - - conda create --name icepyx-env --channel conda-forge python=3.10 proj geos - - source activate icepyx-env - - pip install -r requirements.txt -r requirements-dev.txt - - pip install -e .[complete] - -stages: - - name: basic tests - if: (type = pull_request) OR (type = push AND repo = icesat2py/icepyx AND branch IN (main, development)) - - name: behind Earthdata - if: branch = main OR commit_message =~ nsidc_tests OR type = cron - -#ultimately move basic tests list into a separate script with the list of files to run (then this can be put into a matrix and parallellized as well) -jobs: - include: - - stage: basic tests - script: pytest icepyx/ --verbose --cov app --ignore=icepyx/tests/test_behind_NSIDC_API_login.py --ignore=icepyx/tests/test_auth.py - # includes an integrity check of the uploader as recommended by CodeCov - after_success: - - curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --keyring trustedkeys.gpg --import # One-time step - - curl -Os https://uploader.codecov.io/latest/linux/codecov - - curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM - - curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig - - gpgv codecov.SHA256SUM.sig codecov.SHA256SUM - - shasum -a 256 -c codecov.SHA256SUM - - chmod +x codecov - - ./codecov -t ${CODECOV_TOKEN} - - stage: behind Earthdata - script: - - export EARTHDATA_PASSWORD=$NSIDC_LOGIN - - pytest icepyx/tests/test_behind_NSIDC_API_login.py icepyx/tests/test_auth.py diff --git a/README.rst b/README.rst index 5ef8b1ba7..b89dd51e0 100644 --- a/README.rst +++ b/README.rst @@ -7,9 +7,9 @@ icepyx |JOSS| |Zenodo-all| -Latest release (main branch): |Docs Status main| |Travis main Build Status| |Code Coverage main| +Latest release (main branch): |Docs Status main| |Unit Tests Status (main)| |Integration Tests Status (main)| |Code Coverage main| -Current development version (development branch): |Docs Status dev| |Travis dev Build Status| |Code Coverage dev| |Pre-commit dev| +Current development version (development branch): |Docs Status dev| |Unit Tests Status (dev)| |Integration Tests Status (main)| |Code Coverage dev| |Pre-commit dev| .. |GitHub license| image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg :target: https://opensource.org/licenses/BSD-3-Clause @@ -38,11 +38,17 @@ Current development version (development branch): |Docs Status dev| |Travis dev .. |Docs Status dev| image:: https://readthedocs.org/projects/icepyx/badge/?version=development :target: https://icepyx.readthedocs.io/en/development -.. |Travis main Build Status| image:: https://app.travis-ci.com/icesat2py/icepyx.svg?branch=main - :target: https://app.travis-ci.com/icesat2py/icepyx +.. |Unit Tests Status (main)| image:: https://github.com/icesat2py/icepyx/actions/workflows/unit_test.yml/badge.svg?branch=main + :target: https://github.com/icesat2py/icepyx/actions/workflows/unit_test.yml -.. |Travis dev Build Status| image:: https://app.travis-ci.com/icesat2py/icepyx.svg?branch=development - :target: https://app.travis-ci.com/icesat2py/icepyx +.. |Integration Tests Status (main)| image:: https://github.com/icesat2py/icepyx/actions/workflows/integration_test.yml/badge.svg?branch=main + :target: https://github.com/icesat2py/icepyx/actions/workflows/integration_test.yml + +.. |Unit Tests Status (dev)| image:: https://github.com/icesat2py/icepyx/actions/workflows/unit_test.yml/badge.svg?branch=development + :target: https://github.com/icesat2py/icepyx/actions/workflows/unit_test.yml + +.. |Integration Tests Status (dev)| image:: https://github.com/icesat2py/icepyx/actions/workflows/integration_test.yml/badge.svg?branch=development + :target: https://github.com/icesat2py/icepyx/actions/workflows/integration_test.yml .. |Code Coverage main| image:: https://codecov.io/gh/icesat2py/icepyx/branch/main/graph/badge.svg :target: https://codecov.io/gh/icesat2py/icepyx From 572e48c6c8ccce10d7524516fd0f26d34ddc659b Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Thu, 29 Aug 2024 18:09:45 -0600 Subject: [PATCH 21/31] Extract constant URLs to own module (#591) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: GitHub Action --- .../documentation/packages_user_uml.svg | 160 ++++++++++-------- icepyx/core/granules.py | 13 +- icepyx/core/is2ref.py | 9 +- icepyx/core/urls.py | 10 ++ 4 files changed, 108 insertions(+), 84 deletions(-) create mode 100644 icepyx/core/urls.py diff --git a/doc/source/user_guide/documentation/packages_user_uml.svg b/doc/source/user_guide/documentation/packages_user_uml.svg index 029a13015..2cfe26a67 100644 --- a/doc/source/user_guide/documentation/packages_user_uml.svg +++ b/doc/source/user_guide/documentation/packages_user_uml.svg @@ -4,172 +4,190 @@ - + packages_user_uml - + icepyx.core - -icepyx.core + +icepyx.core icepyx.core.APIformatting - -icepyx.core.APIformatting + +icepyx.core.APIformatting icepyx.core.auth - -icepyx.core.auth + +icepyx.core.auth icepyx.core.exceptions - -icepyx.core.exceptions + +icepyx.core.exceptions icepyx.core.auth->icepyx.core.exceptions - - + + icepyx.core.granules - -icepyx.core.granules + +icepyx.core.granules icepyx.core.granules->icepyx.core.auth - - + + + + + +icepyx.core.urls + +icepyx.core.urls + + + +icepyx.core.granules->icepyx.core.urls + + icepyx.core.icesat2data - -icepyx.core.icesat2data + +icepyx.core.icesat2data - + icepyx.core.icesat2data->icepyx.core.exceptions - - + + icepyx.core.is2ref - -icepyx.core.is2ref + +icepyx.core.is2ref + + + +icepyx.core.is2ref->icepyx.core.urls + + icepyx.core.query - -icepyx.core.query + +icepyx.core.query - + icepyx.core.query->icepyx.core.auth - - + + - + icepyx.core.query->icepyx.core.exceptions - - + + - + icepyx.core.query->icepyx.core.granules - - + + - + icepyx.core.variables - -icepyx.core.variables + +icepyx.core.variables - + icepyx.core.query->icepyx.core.variables - - + + - + icepyx.core.visualization - -icepyx.core.visualization + +icepyx.core.visualization - + icepyx.core.query->icepyx.core.visualization - - + + icepyx.core.read - -icepyx.core.read + +icepyx.core.read - + icepyx.core.read->icepyx.core.auth - - + + - + icepyx.core.read->icepyx.core.exceptions - - + + - + icepyx.core.read->icepyx.core.variables - - + + icepyx.core.spatial - -icepyx.core.spatial + +icepyx.core.spatial icepyx.core.temporal - -icepyx.core.temporal + +icepyx.core.temporal - + icepyx.core.validate_inputs - -icepyx.core.validate_inputs + +icepyx.core.validate_inputs - + icepyx.core.variables->icepyx.core.auth - - + + - + icepyx.core.variables->icepyx.core.exceptions - - + + diff --git a/icepyx/core/granules.py b/icepyx/core/granules.py index 7c748fe6f..37fda87ad 100644 --- a/icepyx/core/granules.py +++ b/icepyx/core/granules.py @@ -14,6 +14,7 @@ import icepyx.core.APIformatting as apifmt from icepyx.core.auth import EarthdataAuthMixin import icepyx.core.exceptions +from icepyx.core.urls import DOWNLOAD_BASE_URL, GRANULE_SEARCH_BASE_URL, ORDER_BASE_URL def info(grans): @@ -202,8 +203,6 @@ def get_avail(self, CMRparams, reqparams, cloud=False): # if not hasattr(self, 'avail'): self.avail = [] - granule_search_url = "https://cmr.earthdata.nasa.gov/search/granules" - headers = {"Accept": "application/json", "Client-Id": "icepyx"} # note we should also check for errors whenever we ping NSIDC-API - # make a function to check for errors @@ -221,7 +220,7 @@ def get_avail(self, CMRparams, reqparams, cloud=False): headers["CMR-Search-After"] = cmr_search_after response = requests.get( - granule_search_url, + GRANULE_SEARCH_BASE_URL, headers=headers, params=apifmt.to_string(params), ) @@ -309,8 +308,6 @@ def place_order( query.Query.order_granules """ - base_url = "https://n5eil02u.ecs.nsidc.org/egi/request" - self.get_avail(CMRparams, reqparams) if subset is False: @@ -346,7 +343,7 @@ def place_order( ) request_params.update({"page_num": page_num}) - request = self.session.get(base_url, params=request_params) + request = self.session.get(ORDER_BASE_URL, params=request_params) # DevGoal: use the request response/number to do some error handling/ # give the user better messaging for failures @@ -378,7 +375,7 @@ def place_order( print("order ID: ", orderID) # Create status URL - statusURL = base_url + "/" + orderID + statusURL = f"{ORDER_BASE_URL}/{orderID}" if verbose is True: print("status URL: ", statusURL) @@ -523,7 +520,7 @@ def download(self, verbose, path, restart=False): i_order = self.orderIDs.index(order_start) + 1 for order in self.orderIDs[i_order:]: - downloadURL = "https://n5eil02u.ecs.nsidc.org/esir/" + order + ".zip" + downloadURL = f"{DOWNLOAD_BASE_URL}/{order}.zip" # DevGoal: get the download_url from the granules if verbose is True: diff --git a/icepyx/core/is2ref.py b/icepyx/core/is2ref.py index 1cd58f10a..95df81971 100644 --- a/icepyx/core/is2ref.py +++ b/icepyx/core/is2ref.py @@ -7,6 +7,8 @@ import numpy as np import requests +from icepyx.core.urls import COLLECTION_SEARCH_BASE_URL, EGI_BASE_URL + # ICESat-2 specific reference functions @@ -81,8 +83,7 @@ def about_product(prod): query.Query.product_all_info """ - cmr_collections_url = "https://cmr.earthdata.nasa.gov/search/collections.json" - response = requests.get(cmr_collections_url, params={"short_name": prod}) + response = requests.get(COLLECTION_SEARCH_BASE_URL, params={"short_name": prod}) results = json.loads(response.content) return results @@ -100,9 +101,7 @@ def _get_custom_options(session, product, version): "Don't forget to log in to Earthdata using query.earthdata_login()" ) - capability_url = ( - f"https://n5eil02u.ecs.nsidc.org/egi/capabilities/{product}.{version}.xml" - ) + capability_url = f"{EGI_BASE_URL}/capabilities/{product}.{version}.xml" response = session.get(capability_url) root = ET.fromstring(response.content) diff --git a/icepyx/core/urls.py b/icepyx/core/urls.py new file mode 100644 index 000000000..8c5bc325b --- /dev/null +++ b/icepyx/core/urls.py @@ -0,0 +1,10 @@ +from typing import Final + +CMR_BASE_URL: Final = "https://cmr.earthdata.nasa.gov" +GRANULE_SEARCH_BASE_URL: Final = f"{CMR_BASE_URL}/search/granules" +COLLECTION_SEARCH_BASE_URL: Final = f"{CMR_BASE_URL}/search/collections.json" + +EGI_BASE_URL: Final = "https://n5eil02u.ecs.nsidc.org/egi" +ORDER_BASE_URL: Final = f"{EGI_BASE_URL}/request" + +DOWNLOAD_BASE_URL: Final = "https://n5eil02u.ecs.nsidc.org/esir" From 6d6a085481af11a61720d801996d5922c2b843c1 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Wed, 4 Sep 2024 09:40:39 +1200 Subject: [PATCH 22/31] Reinstate test_download_granules_without_subsetting (#581) Ensure that granules can be ordered from NSIDC and downloaded with the `subset=False` option. Also fix a possible race condition in case the NSIDC order status is completed right at the start (e.g. when order was cached/done already). Co-authored-by: Jessica Scheick --- icepyx/core/granules.py | 5 +++ icepyx/tests/test_behind_NSIDC_API_login.py | 47 ++++++++++++++++++--- 2 files changed, 47 insertions(+), 5 deletions(-) diff --git a/icepyx/core/granules.py b/icepyx/core/granules.py index 37fda87ad..b29a147e1 100644 --- a/icepyx/core/granules.py +++ b/icepyx/core/granules.py @@ -396,6 +396,11 @@ def place_order( status = statuslist[0] print("Initial status of your order request at NSIDC is: ", status) + # If status is already finished without going into pending/processing + if status.startswith("complete"): + loop_response = self.session.get(statusURL) + loop_root = ET.fromstring(loop_response.content) + # Continue loop while request is still processing while status == "pending" or status == "processing": print( diff --git a/icepyx/tests/test_behind_NSIDC_API_login.py b/icepyx/tests/test_behind_NSIDC_API_login.py index b3824030e..f9fb49077 100644 --- a/icepyx/tests/test_behind_NSIDC_API_login.py +++ b/icepyx/tests/test_behind_NSIDC_API_login.py @@ -1,3 +1,8 @@ +""" +Integration tests that require authentication to Earthdata login. +""" + +import glob import json import os @@ -49,8 +54,40 @@ def test_download_granules_with_subsetting(reg, session): reg.download_granules(path) -# def test_download_granules_without_subsetting(reg_a, session): -# path = './downloads' -# reg_a.order_granules(session, subset=False) -# reg_a.download_granules(session, path) -# #check that the max extent of the downloaded granules isn't subsetted +def test_download_granules_without_subsetting(reg, session, capsys): + """ + Test that granules can be ordered from NSIDC and downloaded with the `subset=False` + option. + """ + path = "./downloads" + + reg.order_granules(verbose=False, subset=False, email=False) + out, err = capsys.readouterr() # capture stdout and stderr + assert out.startswith( + "Total number of data order requests is 1 for 3 granules.\n" + "Data request 1 of 1 is submitting to NSIDC\n" + ) + assert err == "" + + assert reg.reqparams == { + "client_string": "icepyx", + "include_meta": "Y", + "page_num": 0, + "page_size": 2000, + "request_mode": "async", + "short_name": "ATL06", + "version": "006", + } + assert len(reg.granules.orderIDs) == 2 + assert int(reg.granules.orderIDs[0]) >= 5_000_000_000_000 + + reg.download_granules(path=path) + # check that there are the right number of files of the correct size + assert len(glob.glob(pathname=f"{path}/ATL06_201902*.iso.xml")) == 3 + h5_paths = sorted(glob.glob(pathname=f"{path}/ATL06_201902*.h5")) + assert len(h5_paths) == 3 + assert [os.path.getsize(filename=p) for p in h5_paths] == [ + 53228429, # 50.8 MiB + 65120027, # 62.1 MiB + 49749227, # 47.4 MiB + ] From 418c9e7f294940831233ec9c3f9b055b4f2d5ca3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 5 Sep 2024 18:00:18 -0400 Subject: [PATCH 23/31] Bump sangonzal/repository-traffic-action from 0.1.5 to 1 in the github-actions group (#596) --- .github/workflows/traffic_action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/traffic_action.yml b/.github/workflows/traffic_action.yml index 48db62741..333ec2d5a 100644 --- a/.github/workflows/traffic_action.yml +++ b/.github/workflows/traffic_action.yml @@ -23,7 +23,7 @@ jobs: # Calculates traffic and clones and stores in CSV file - name: GitHub traffic - uses: sangonzal/repository-traffic-action@v0.1.5 + uses: sangonzal/repository-traffic-action@v1 env: TRAFFIC_ACTION_TOKEN: ${{ secrets.TRAFFIC_ACTION_TOKEN }} From dbaff0e6ab6280df7877a23e4c739c37bdfe6afb Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 5 Sep 2024 16:14:24 -0600 Subject: [PATCH 24/31] [pre-commit.ci] pre-commit autoupdate (#597) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jessica Scheick --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 934cdbb97..cbb4ad81d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -26,14 +26,14 @@ repos: - tomli - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.0 + rev: v0.6.3 hooks: - id: ruff args: ["--fix", "--show-fixes"] - id: ruff-format - repo: https://github.com/abravalheri/validate-pyproject - rev: v0.18 + rev: v0.19 hooks: - id: validate-pyproject From 054fbe4df00dc117cdf33c3ae1dd1b6f02585903 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 9 Sep 2024 14:28:04 -0400 Subject: [PATCH 25/31] bump sangonzal/repository-traffic-action version to latest working one (fixes #596) (#601) dependabot bumped to an invalid version --- .github/workflows/traffic_action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/traffic_action.yml b/.github/workflows/traffic_action.yml index 333ec2d5a..50a7312d7 100644 --- a/.github/workflows/traffic_action.yml +++ b/.github/workflows/traffic_action.yml @@ -23,7 +23,7 @@ jobs: # Calculates traffic and clones and stores in CSV file - name: GitHub traffic - uses: sangonzal/repository-traffic-action@v1 + uses: sangonzal/repository-traffic-action@v0.1.6 env: TRAFFIC_ACTION_TOKEN: ${{ secrets.TRAFFIC_ACTION_TOKEN }} From 1cf650486c6220b355bc1f0350f41e4167be4a61 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 9 Sep 2024 14:33:38 -0400 Subject: [PATCH 26/31] bump sangonzal/repository-traffic-action version to latest working one (fixes #596 + #601) (#602) --- .github/workflows/traffic_action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/traffic_action.yml b/.github/workflows/traffic_action.yml index 50a7312d7..15f153bed 100644 --- a/.github/workflows/traffic_action.yml +++ b/.github/workflows/traffic_action.yml @@ -23,7 +23,7 @@ jobs: # Calculates traffic and clones and stores in CSV file - name: GitHub traffic - uses: sangonzal/repository-traffic-action@v0.1.6 + uses: sangonzal/repository-traffic-action@v.0.1.6 env: TRAFFIC_ACTION_TOKEN: ${{ secrets.TRAFFIC_ACTION_TOKEN }} From 2566d9626b137f06f599bd4ebfe37015bae00b81 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Thu, 12 Sep 2024 10:59:30 -0400 Subject: [PATCH 27/31] [docs] traffic updates May-Aug 2024 (#606) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --- doc/source/tracking/pypistats/downloads.svg | 2753 ++--- .../tracking/pypistats/downloads_data.csv | 245 + .../tracking/pypistats/sys_downloads_data.csv | 319 + doc/source/tracking/traffic/clones.csv | 91 + doc/source/tracking/traffic/plots.svg | 9025 +++++++++-------- doc/source/tracking/traffic/views.csv | 118 + 6 files changed, 6918 insertions(+), 5633 deletions(-) diff --git a/doc/source/tracking/pypistats/downloads.svg b/doc/source/tracking/pypistats/downloads.svg index 484dc6d7f..410c2a02e 100644 --- a/doc/source/tracking/pypistats/downloads.svg +++ b/doc/source/tracking/pypistats/downloads.svg @@ -6,11 +6,11 @@ - 2024-05-01T20:57:00.508010 + 2024-09-01T20:56:47.103398 image/svg+xml - Matplotlib v3.8.4, https://matplotlib.org/ + Matplotlib v3.9.2, https://matplotlib.org/ @@ -41,12 +41,12 @@ z - - + @@ -205,12 +205,12 @@ z - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - + - - + + - + - - - + + + - + - + - + - - + + - + - - - + + + - + - + - + - - + + - + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -424,11 +422,33 @@ z - + + + + + + + + + + + + + + + + + + + + + + + - + @@ -547,1260 +567,1383 @@ z - + - - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + - - + + - + - + @@ -2165,7 +2308,7 @@ z - + diff --git 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b/doc/source/tracking/pypistats/sys_downloads_data.csv index cb8ff00c5..86c89887a 100644 --- a/doc/source/tracking/pypistats/sys_downloads_data.csv +++ b/doc/source/tracking/pypistats/sys_downloads_data.csv @@ -211,6 +211,33 @@ Darwin,2024-04-10,2 Darwin,2024-04-12,2 Darwin,2024-04-25,2 Darwin,2024-04-29,1 +Darwin,2024-05-03,2 +Darwin,2024-05-21,2 +Darwin,2024-05-22,2 +Darwin,2024-05-27,2 +Darwin,2024-05-29,2 +Darwin,2024-05-31,2 +Darwin,2024-06-01,2 +Darwin,2024-06-03,2 +Darwin,2024-06-04,1 +Darwin,2024-06-05,4 +Darwin,2024-06-06,2 +Darwin,2024-06-07,4 +Darwin,2024-06-10,2 +Darwin,2024-06-11,2 +Darwin,2024-06-13,3 +Darwin,2024-06-18,1 +Darwin,2024-07-06,2 +Darwin,2024-07-14,2 +Darwin,2024-07-16,3 +Darwin,2024-07-29,1 +Darwin,2024-07-31,2 +Darwin,2024-08-08,1 +Darwin,2024-08-10,5 +Darwin,2024-08-12,1 +Darwin,2024-08-14,2 +Darwin,2024-08-20,2 +Darwin,2024-08-21,2 Linux,2020-06-18,9 Linux,2020-06-19,2 Linux,2020-06-22,2 @@ -1128,6 +1155,122 @@ Linux,2024-04-27,12 Linux,2024-04-28,18 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+Linux,2024-06-22,22 +Linux,2024-06-23,18 +Linux,2024-06-24,29 +Linux,2024-06-25,25 +Linux,2024-06-26,67 +Linux,2024-06-27,41 +Linux,2024-06-28,10 +Linux,2024-06-29,10 +Linux,2024-06-30,1 +Linux,2024-07-01,26 +Linux,2024-07-02,43 +Linux,2024-07-03,48 +Linux,2024-07-04,30 +Linux,2024-07-05,26 +Linux,2024-07-06,11 +Linux,2024-07-07,2 +Linux,2024-07-08,74 +Linux,2024-07-09,47 +Linux,2024-07-10,38 +Linux,2024-07-11,26 +Linux,2024-07-12,30 +Linux,2024-07-13,4 +Linux,2024-07-14,5 +Linux,2024-07-15,32 +Linux,2024-07-16,37 +Linux,2024-07-17,58 +Linux,2024-07-18,31 +Linux,2024-07-19,44 +Linux,2024-07-20,5 +Linux,2024-07-22,52 +Linux,2024-07-23,77 +Linux,2024-07-24,40 +Linux,2024-07-25,43 +Linux,2024-07-26,48 +Linux,2024-07-27,22 +Linux,2024-07-28,27 +Linux,2024-07-29,38 +Linux,2024-07-30,50 +Linux,2024-07-31,48 +Linux,2024-08-01,98 +Linux,2024-08-02,70 +Linux,2024-08-03,76 +Linux,2024-08-04,46 +Linux,2024-08-05,95 +Linux,2024-08-06,75 +Linux,2024-08-07,88 +Linux,2024-08-08,57 +Linux,2024-08-09,69 +Linux,2024-08-10,62 +Linux,2024-08-11,8 +Linux,2024-08-12,50 +Linux,2024-08-13,25 +Linux,2024-08-14,68 +Linux,2024-08-15,63 +Linux,2024-08-16,55 +Linux,2024-08-17,8 +Linux,2024-08-18,6 +Linux,2024-08-19,43 +Linux,2024-08-20,46 +Linux,2024-08-21,58 +Linux,2024-08-22,40 +Linux,2024-08-23,44 +Linux,2024-08-24,14 +Linux,2024-08-25,12 +Linux,2024-08-26,20 +Linux,2024-08-27,10 +Linux,2024-08-28,16 +Linux,2024-08-29,38 +Linux,2024-08-30,8 +Linux,2024-08-31,6 Windows,2020-06-21,1 Windows,2020-06-25,1 Windows,2020-06-30,1 @@ -1894,6 +2037,97 @@ Windows,2024-04-27,1 Windows,2024-04-28,15 Windows,2024-04-29,4 Windows,2024-04-30,2 +Windows,2024-05-01,4 +Windows,2024-05-02,1 +Windows,2024-05-03,5 +Windows,2024-05-04,2 +Windows,2024-05-05,2 +Windows,2024-05-06,4 +Windows,2024-05-07,2 +Windows,2024-05-08,4 +Windows,2024-05-09,5 +Windows,2024-05-10,7 +Windows,2024-05-13,10 +Windows,2024-05-15,9 +Windows,2024-05-16,1 +Windows,2024-05-19,7 +Windows,2024-05-20,6 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+Windows,2024-07-17,2 +Windows,2024-07-18,8 +Windows,2024-07-19,3 +Windows,2024-07-20,1 +Windows,2024-07-24,2 +Windows,2024-07-25,7 +Windows,2024-07-27,10 +Windows,2024-07-29,5 +Windows,2024-07-30,4 +Windows,2024-08-01,27 +Windows,2024-08-05,4 +Windows,2024-08-06,2 +Windows,2024-08-07,7 +Windows,2024-08-08,3 +Windows,2024-08-09,9 +Windows,2024-08-10,2 +Windows,2024-08-11,2 +Windows,2024-08-12,4 +Windows,2024-08-13,2 +Windows,2024-08-19,4 +Windows,2024-08-20,6 +Windows,2024-08-21,15 +Windows,2024-08-22,5 +Windows,2024-08-23,2 +Windows,2024-08-25,2 +Windows,2024-08-26,6 +Windows,2024-08-27,7 +Windows,2024-08-28,2 +Windows,2024-08-29,2 +Windows,2024-08-30,2 +Windows,2024-08-31,2 null,2020-06-18,12 null,2020-06-19,12 null,2020-06-21,2 @@ -2739,3 +2973,88 @@ null,2024-04-26,2 null,2024-04-27,1 null,2024-04-29,17 null,2024-04-30,1 +null,2024-05-01,1 +null,2024-05-02,5 +null,2024-05-04,3 +null,2024-05-05,13 +null,2024-05-06,2 +null,2024-05-07,2 +null,2024-05-08,2 +null,2024-05-11,1 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+2024-09-07,28,5 +2024-09-08,23,3 +2024-09-09,44,7 From bea9fe04c95b83eddec84dfcc77d38f454c15cf0 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Fri, 13 Sep 2024 12:48:08 -0600 Subject: [PATCH 28/31] Drop support for Python 3.7 and 3.8 (#608) --- pyproject.toml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e1ea8ed90..f44ea450a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ description = "Python tools for obtaining and working with ICESat-2 data" license = {file = "LICENSE"} readme = "README.rst" -requires-python = "~=3.7" +requires-python = ">=3.9" dynamic = ["version", "dependencies"] authors = [ @@ -20,8 +20,6 @@ classifiers=[ "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", From a98409ff5fd5d971c712e50585d90a36cc95ac52 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Mon, 16 Sep 2024 11:33:47 -0600 Subject: [PATCH 29/31] Add v1.x deprecation warning (#603) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jessica Scheick Co-authored-by: Jessica Scheick --- icepyx/__init__.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/icepyx/__init__.py b/icepyx/__init__.py index a9d61834b..b0cd8095d 100644 --- a/icepyx/__init__.py +++ b/icepyx/__init__.py @@ -1,3 +1,17 @@ +from warnings import warn + +deprecation_msg = """icepyx v1.x is being deprecated; the back-end systems on which it relies +will be shut down as of late 2024. At that time, upgrade to icepyx v2.x, which uses the +new NASA Harmony back-end, will be required. Please see + for more +information! +""" +# IMPORTANT: This is being done before the other icepyx imports because the imported +# code changes warning filters. If this is done after the imports, the warning won't +# work. +warn(deprecation_msg, FutureWarning, stacklevel=2) + + from _icepyx_version import version as __version__ from icepyx.core.query import GenQuery, Query From 143966956fdf664e0d4a98fc9f5d4aa2e9c98b81 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Mon, 16 Sep 2024 12:38:29 -0600 Subject: [PATCH 30/31] Replace integration test review trigger with manual trigger (#595) --- .github/workflows/integration_test.yml | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/.github/workflows/integration_test.yml b/.github/workflows/integration_test.yml index 1c9dc6ed7..4bc27655e 100644 --- a/.github/workflows/integration_test.yml +++ b/.github/workflows/integration_test.yml @@ -6,33 +6,29 @@ on: push: branches: - "main" # Releases - - "development" # PR merges + - "development" # Feature PR merges pull_request: branches: - - "main" # Release pull requests - pull_request_review: - types: - - "submitted" - paths: - - ".github/**" - - "icepyx/**/*.py" - - "pyproject.toml" - - "requirements*.txt" + - "main" # Release PRs + workflow_dispatch: + inputs: + ref: + description: "The ref to test" + type: "string" jobs: test: name: "Integration test" - # Job is conditional: - # - Do not run on PRs from forks - # - Do not run on `pull_request_review` events unless the PR is approved. - if: "${{ !github.event.pull_request.head.repo.fork && (github.event.action != 'pull_request_review' || github.event.review.state == 'approved') }}" + # Do not run on PRs from forks: + if: "${{ !github.event.pull_request.head.repo.fork }}" runs-on: "ubuntu-latest" steps: - uses: "actions/checkout@v4" with: fetch-depth: 0 + ref: "${{ inputs.ref }}" - uses: "./.github/actions/install-icepyx" with: From 2495978ae2db8ae3932ec12fe0bcc27e86451365 Mon Sep 17 00:00:00 2001 From: Jessica Scheick Date: Mon, 16 Sep 2024 14:55:14 -0400 Subject: [PATCH 31/31] release v1.3.0 (#607) Co-authored-by: Matt Fisher --- doc/source/user_guide/changelog/index.rst | 10 ++- doc/source/user_guide/changelog/v1.3.0.rst | 81 ++++++++++++++++++++++ 2 files changed, 90 insertions(+), 1 deletion(-) create mode 100644 doc/source/user_guide/changelog/v1.3.0.rst diff --git a/doc/source/user_guide/changelog/index.rst b/doc/source/user_guide/changelog/index.rst index 927bc497f..491de3708 100644 --- a/doc/source/user_guide/changelog/index.rst +++ b/doc/source/user_guide/changelog/index.rst @@ -7,9 +7,17 @@ This is the list of changes made to icepyx in between each release. Full details can be found in the `commit logs `_. -Latest Release (Version 1.2.0) +Latest Release (Version 1.3.0) ------------------------------ +.. toctree:: + :maxdepth: 2 + + v1.3.0 + +Version 1.2.0 +------------- + .. toctree:: :maxdepth: 2 diff --git a/doc/source/user_guide/changelog/v1.3.0.rst b/doc/source/user_guide/changelog/v1.3.0.rst new file mode 100644 index 000000000..142b0eb27 --- /dev/null +++ b/doc/source/user_guide/changelog/v1.3.0.rst @@ -0,0 +1,81 @@ +What's new in 1.3.0 (13 September 2024) +--------------------------------------- + +These are the changes in icepyx 1.3.0 See :ref:`release` for a full changelog +including other versions of icepyx. + +.. warning:: + This is anticipated to be the last release in v1 of icepyx. + + NSIDC (the NASA DAAC that hosts ICESat-2 data) is transitioning their + API endpoint from the on-premises EGI system to the cloud-based Harmony services. + icepyx is being updated to access these new services; the only change users + will experience concerns services that are no longer available (e.g. reformatting). + + The developers plan to use this version change to implement additional breaking + changes concerning the Query module, transitioning it's functionality to use + the earthaccess library instead. + + Find more details on all these changes, including their progress, on GitHub issues and discussions. + + +Bug fixes +~~~~~~~~~ + +- Bugfix: catch multiple types of exceptions (#560) + + +Deprecations +~~~~~~~~~~~~ + +- Drop support for Python 3.7 and 3.8 (#608) +- Add v1.x deprecation warning (#603) + + +Maintenance +^^^^^^^^^^^ + +- Avoid running tests that require creds on PRs (#563) + + - enables PRs from forks to pass CI tests and be merged + +- Skip linting and formatting Jupyter Notebooks for now (#567) +- Keep GitHub Actions up to date with GitHub's Dependabot (#555) +- Bump the github-actions group with 3 updates (#568) +- Add codespell spelling/typo linter and fix errors (#556) +- Validate pyproject.toml (#557) +- Enable currently-ignored linting rules E721, E722, F403 (#573) +- Add ruff rules C4 to check comprehensions (#570) +- Add ruff rules SIM to simplify Python code (#572) +- More ruff & pre-commit rules (#546) +- Fix minor typo (#589) +- Extract constant URLs to own module (#591) +- Clarify some comments / docstrings (#592) +- Migrate unit and integration tests from TravisCI to GitHub Actions (#580) +- Reinstate test_download_granules_without_subsetting (#581) + + - Ensure that granules can be ordered from NSIDC and downloaded with the `subset=False` option. + - Also fix a possible race condition in case the NSIDC order status is completed right at the start (e.g. when order was cached/done already). + +- Bump sangonzal/repository-traffic-action from 0.1.5 to 1 in the github-actions group (#596) +- [pre-commit.ci] pre-commit autoupdate (#597) +- bump sangonzal/repository-traffic-action version to latest working one (fixes #596) (#601) +- Replace integration test review trigger with manual trigger (#595) + + +Documentation +^^^^^^^^^^^^^ + +- Update viz doc to clarify its current status (partial functionality - incompatible with OA API changes) (#540) +- Add quickstart to README (#549) +- docs: add cclauss as a contributor for maintenance and review (#583) +- docs: add jrenrut as a contributor for bug, and code (#586) +- docs: add mfisher87 as a contributor for bug, code, and 4 more (#585) +- Tweak format and wording of contributor doc (#566) +- [docs] traffic updates May-Aug 2024 (#606) + + +Contributors +~~~~~~~~~~~~ + +.. contributors:: v1.2.0..v1.3.0|HEAD