From 1b7343bfc51733d382145f801a58141a66fc7c3c Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 29 Jun 2024 21:59:35 -0600 Subject: [PATCH 01/38] Specify dependency groups in a way that doesn't require poetry Poetry is required to use dependency groups. To make things compatible with other ways of dependency management, switch to PEP621 optional dependencies, but specified using the Poetry configuration aliases to retain support for poetry. TODO: Docs --- pyproject.toml | 103 ++++++++++++++++++++++++++++++++----------------- 1 file changed, 67 insertions(+), 36 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index fe872af5..3e4c3b94 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -43,6 +43,14 @@ s3fs = ">=2022.11" fsspec = ">=2022.11" tinynetrc = "^1.3.1" multimethod = ">=1.8" +importlib-resources = ">=6.3.2" +typing_extensions = ">=4.10.0" + +## Optional dependencies; can be opted-in with extra specifications below +## This is so verbose because Poetry requires it: https://python-poetry.org/docs/pyproject#extras +## If we switch to PEP621 specification, we can specify extras (called +## "optional" under PEP621) with versions in one line: +#https://peps.python.org/pep-0621/#example kerchunk = { version = ">=0.1.2", optional = true } # kerchunk requires numpy, but numpy >=1.26.0 is required for Python 3.12 support numpy = [ @@ -50,48 +58,47 @@ numpy = [ { version = ">=1.26.0", optional = true, python = ">=3.12" } ] dask = { version = ">=2022.1.0", optional = true } -importlib-resources = ">=6.3.2" -typing_extensions = ">=4.10.0" - -[tool.poetry.extras] -kerchunk = ["kerchunk", "dask"] -[tool.poetry.group.dev.dependencies] -python-magic = ">=0.4" -mypy = ">=0.812" -jupyterlab = ">=3" -pre-commit = ">=2.4" -pytest = ">=6.0" -pytest-cov = ">=2.8" -pytest-watch = ">=4.2" +# Dev +bump-my-version = { version = ">=0.10.0", optional = true } +pre-commit = { version = ">=2.4", optional = true } +ruff = { version = ">=0.4.2", optional = true } + +# Test +mypy = { version = ">=0.812", optional = true } +pytest = { version = ">=6.0", optional = true } +pytest-cov = { version = ">=2.8", optional = true } +pytest-watch = { version = ">=4.2", optional = true } +python-magic = { version = ">=0.4", optional = true } +responses = { version = ">=0.14", optional = true } +types-requests = { version = ">=0.1", optional = true } +types-setuptools = { version = ">=0.1", optional = true } +vcrpy = { version = ">=6.0.1", optional = true } + +# Docs +jupyterlab = { version = ">=3", optional = true } +ipywidgets = { version = ">=7.7.0", optional = true } +widgetsnbextension = { version = ">=3.6.0", optional = true } # Prevent install of 1.6.0 because the module mkdocs.tests # is no longer exported, which causes mkdocs-jupyter to # break with a ModuleNotFoundError. -mkdocs = ">=1.2,!=1.6.0" -mkdocs-material = ">=7.1,<10.0" -mkdocs-redirects = ">=1.2.1" -markdown-callouts = ">=0.2.0" -markdown-include = ">=0.6" -mkdocstrings = {extras = ["python"], version = ">=0.19.0"} -mkdocs-jupyter = ">=0.19.0" -pymdown-extensions = ">=9.2" -pygments = ">=2.11.1" -responses = ">=0.14" -ruff = ">=0.4.2" -types-requests = ">=0.1" -types-setuptools = ">=0.1" -ipywidgets = ">=7.7.0" -widgetsnbextension = ">=3.6.0" +mkdocs = { version = ">=1.2,!=1.6.0", optional = true } +mkdocs-material = { version = ">=7.1,<10.0", optional = true } +mkdocs-redirects = { version = ">=1.2.1", optional = true } +markdown-callouts = { version = ">=0.2.0", optional = true } +markdown-include = { version = ">=0.6", optional = true } +mkdocstrings = {extras = ["python"], version = ">=0.19.0", optional = true} +mkdocs-jupyter = { version = ">=0.19.0", optional = true } +pymdown-extensions = { version = ">=9.2", optional = true } +pygments = { version = ">=2.11.1", optional = true } # for notebook integrations and documentation examples -xarray = ">=2023.01" -matplotlib = ">=3.3" -h5netcdf = ">=0.11" +xarray = { version = ">=2023.01", optional = true } +matplotlib = { version = ">=3.3", optional = true } +h5netcdf = { version = ">=0.11", optional = true } pyproj = [ - { version = ">=3.5.0", python = "<3.12" }, - { version = ">=3.6.1", python = ">=3.12" } + { version = ">=3.5.0", python = "<3.12", optional = true }, + { version = ">=3.6.1", python = ">=3.12", optional = true }, ] -bump-my-version = ">=0.10.0" -vcrpy = ">=6.0.1" # The following error occurs when building the docs, so we must explicitly # include lxml-html-clean as a dev dependency until mkdocs-jupyter is updated: # @@ -100,7 +107,31 @@ vcrpy = ">=6.0.1" # # See https://github.com/danielfrg/mkdocs-jupyter/issues/200 # See https://github.com/danielfrg/mkdocs-jupyter/issues/197 -lxml-html-clean = ">=0.1.1" +lxml-html-clean = {version = ">=0.1.1", optional = true} + +[tool.poetry.extras] +kerchunk = ["kerchunk", "dask"] +dev = ["bump-my-version", "pre-commit", "ruff"] +test = ["mypy", "pytest", "pytest-cov", "pytest-watch", "python-magic", "responses", "types-requests", "types-setuptools", "vcrpy"] +docs = [ + "jupyterlab", + "mkdocs", + "mkdocs-material", + "mkdocs-redirects", + "markdown-callouts", + "markdown-include", + "mkdocstrings", + "mkdocs-jupyter", + "pymdown-extensions", + "ipywidgets", + "widetsnbextension", + "xarray", + "matplotlib", + "h5netcdf", + "pyproj", +] + +[tool.poetry.group.dev.dependencies] [build-system] requires = ["poetry-core>=1.0.0"] From f2e15ce7ad2af34a4df07a5989a6c34a405fb973 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 29 Jun 2024 22:33:09 -0600 Subject: [PATCH 02/38] Add new poetry hooks As long as we're using it we should be validating! :) --- .pre-commit-config.yaml | 8 ++++++++ pyproject.toml | 2 +- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0832d588..e9fbe175 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -27,6 +27,14 @@ repos: - id: no-commit-to-branch # protects `main` by default - id: trailing-whitespace + - repo: https://github.com/python-poetry/poetry + rev: '1.8.3' + hooks: + - id: poetry-check + # This hook is very slow! Run with `pre-commit run -a poetry-lock --hook-stage manual` + - id: poetry-lock + stages: [manual] + - repo: https://github.com/astral-sh/ruff-pre-commit rev: v0.6.3 hooks: diff --git a/pyproject.toml b/pyproject.toml index 3e4c3b94..7ab15b15 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -124,7 +124,7 @@ docs = [ "mkdocs-jupyter", "pymdown-extensions", "ipywidgets", - "widetsnbextension", + "widgetsnbextension", "xarray", "matplotlib", "h5netcdf", From 732abd17bf56567ccd61753a65555a7a9d1d3df2 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 29 Jun 2024 22:33:47 -0600 Subject: [PATCH 03/38] Update Python compatibility in README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1cad47f3..ad7252db 100644 --- a/README.md +++ b/README.md @@ -82,7 +82,7 @@ Visit [our quick start guide](https://earthaccess.readthedocs.io/en/latest/quick ## Compatibility -Only **Python 3.8+** is supported. +Only **Python 3.9+** is supported. ## How to Contribute to `earthaccess` From a31b7aeed4af95ca50ca4fcf6591954e8326e79f Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 29 Jun 2024 22:36:01 -0600 Subject: [PATCH 04/38] Attempt to fix tests by installing test dependencies --- .github/workflows/integration-test.yml | 8 ++++---- .github/workflows/test.yml | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index e0e3ca07..b5eead1d 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -54,14 +54,14 @@ jobs: - name: Ensure cache is healthy if: steps.cache.outputs.cache-hit == 'true' run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv - - name: Install Dependencies + - name: Install dependencies if: ${{ !env.ACT }} - run: poetry install - - name: Install Dependencies + run: poetry install -E test + - name: Install dependencies if: ${{ env.ACT }} # When using `act` to run the workflow locally, the `poetry install` command # may fail due to network issues when running multiple Docker containers. - run: poetry install || poetry install || poetry install + run: poetry install -E test || poetry install -E test || poetry install -E test - name: Test env: EARTHDATA_USERNAME: ${{ secrets.EDL_USERNAME }} diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index d05453fb..6cf0c203 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -42,14 +42,14 @@ jobs: - name: Ensure cache is healthy if: steps.cache.outputs.cache-hit == 'true' run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv - - name: Install Dependencies + - name: Install dependencies if: ${{ !env.ACT }} - run: poetry install - - name: Install Dependencies + run: poetry install -E test + - name: Install dependencies if: ${{ env.ACT }} # When using `act` to run the workflow locally, the `poetry install` command # may fail due to network issues when running multiple Docker containers. - run: poetry install || poetry install || poetry install + run: poetry install -E test || poetry install -E test || poetry install -E test - name: Test run: poetry run bash scripts/test.sh - name: Upload coverage From 5704abb7543848c50f635bf2fe010248eca28511 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 29 Jun 2024 22:42:32 -0600 Subject: [PATCH 05/38] Decouple test, lint, typecheck scripts Maybe we could use Nox instead of scripts at some point? Then the behaviors can be coupled to the correct environments. --- .github/workflows/test.yml | 2 ++ scripts/lint.sh | 1 - scripts/test.sh | 1 - scripts/typecheck.sh | 5 +++++ 4 files changed, 7 insertions(+), 2 deletions(-) create mode 100644 scripts/typecheck.sh diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 6cf0c203..459e1601 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -50,6 +50,8 @@ jobs: # When using `act` to run the workflow locally, the `poetry install` command # may fail due to network issues when running multiple Docker containers. run: poetry install -E test || poetry install -E test || poetry install -E test + - name: Typecheck + run: poetry run bash scripts/typecheck.sh - name: Test run: poetry run bash scripts/test.sh - name: Upload coverage diff --git a/scripts/lint.sh b/scripts/lint.sh index 02f9c70a..61324ea6 100755 --- a/scripts/lint.sh +++ b/scripts/lint.sh @@ -2,5 +2,4 @@ set -ex -mypy earthaccess stubs tests ruff check . diff --git a/scripts/test.sh b/scripts/test.sh index b8709814..1c74c349 100755 --- a/scripts/test.sh +++ b/scripts/test.sh @@ -4,4 +4,3 @@ set -e set -x pytest tests/unit --cov=earthaccess --cov=tests --cov-report=term-missing "${@}" -s --tb=native --log-cli-level=INFO -bash ./scripts/lint.sh diff --git a/scripts/typecheck.sh b/scripts/typecheck.sh new file mode 100644 index 00000000..bf70d03c --- /dev/null +++ b/scripts/typecheck.sh @@ -0,0 +1,5 @@ +#!/usr/bin/env bash + +set -ex + +mypy earthaccess stubs tests From 82189e7103277a65215893b3b24f79b127015b88 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 29 Jun 2024 22:44:00 -0600 Subject: [PATCH 06/38] Remove redundant config These settings are already specified in pyproject.toml --- scripts/typecheck.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/typecheck.sh b/scripts/typecheck.sh index bf70d03c..012073da 100644 --- a/scripts/typecheck.sh +++ b/scripts/typecheck.sh @@ -2,4 +2,4 @@ set -ex -mypy earthaccess stubs tests +mypy . From 5b819a3cbbb7cab67ecec92d85b696f45e09c581 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 29 Jun 2024 22:48:54 -0600 Subject: [PATCH 07/38] Avoid duplicate test workflow runs Closes #734 --- .github/workflows/test.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 459e1601..7f81e00a 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -2,6 +2,8 @@ name: Unit Tests on: push: + branches: + - main pull_request: types: [opened, synchronize] From 21be5f2246f83981fe259fbba3a5e2fd03a6a2b1 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 29 Jun 2024 22:53:35 -0600 Subject: [PATCH 08/38] Install docs dependencies during readthedocs build --- readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/readthedocs.yml b/readthedocs.yml index 86d9a434..12df42af 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -25,7 +25,7 @@ build: post_install: # Install dependencies with 'docs' dependency group # https://python-poetry.org/docs/managing-dependencies/#dependency-groups - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install -E docs - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry env info - pip freeze From 24a5191478e0276612be8ae630aa0c7dea7bab48 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 3 Sep 2024 20:25:15 -0600 Subject: [PATCH 09/38] Migrate poetry dependency specification to standardized specification --- pyproject.toml | 150 +++++++++++++++++++++---------------------------- 1 file changed, 64 insertions(+), 86 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7ab15b15..975f7a4b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,107 +31,85 @@ classifiers = [ "License :: OSI Approved :: MIT License", ] +requires-python = ">=3.9" + # NOTE: Minimum dependencies are tested with the packages defined in the # `ci/environment-mindeps.yaml` conda environment. When updating minimum dependencies # here, make sure to also update `ci/environment-mindeps.yaml`. -[tool.poetry.dependencies] -python = ">=3.9,<4.0" -python-cmr = ">=0.10.0" -pqdm = ">=0.1" -requests = ">=2.26" -s3fs = ">=2022.11" -fsspec = ">=2022.11" -tinynetrc = "^1.3.1" -multimethod = ">=1.8" -importlib-resources = ">=6.3.2" -typing_extensions = ">=4.10.0" +dependencies = [ + "python-cmr >=0.10.0", + "pqdm >=0.1", + "requests >=2.26", + "s3fs >=2022.11", + "fsspec >=2022.11", + "tinynetrc ^1.3.1", + "multimethod >=1.8", + "importlib-resources >=6.3.2", + "typing_extensions >=4.10.0", + "numpy >=1.24.0;python<3.12", + "numpy >=1.26.0;python>=3.12", +] ## Optional dependencies; can be opted-in with extra specifications below ## This is so verbose because Poetry requires it: https://python-poetry.org/docs/pyproject#extras ## If we switch to PEP621 specification, we can specify extras (called ## "optional" under PEP621) with versions in one line: #https://peps.python.org/pep-0621/#example -kerchunk = { version = ">=0.1.2", optional = true } # kerchunk requires numpy, but numpy >=1.26.0 is required for Python 3.12 support -numpy = [ - { version = ">=1.24.0", optional = true, python = "<3.12" }, - { version = ">=1.26.0", optional = true, python = ">=3.12" } +[project.optional-dependencies] +kerchunk = [ + "kerchunk >=2022.1.0", + "dask >=0.1.2", +] +dev = [ + "bump-my-version >=0.10.0", + "pre-commit >=2.4", + "ruff >=0.4.2", ] -dask = { version = ">=2022.1.0", optional = true } - -# Dev -bump-my-version = { version = ">=0.10.0", optional = true } -pre-commit = { version = ">=2.4", optional = true } -ruff = { version = ">=0.4.2", optional = true } - -# Test -mypy = { version = ">=0.812", optional = true } -pytest = { version = ">=6.0", optional = true } -pytest-cov = { version = ">=2.8", optional = true } -pytest-watch = { version = ">=4.2", optional = true } -python-magic = { version = ">=0.4", optional = true } -responses = { version = ">=0.14", optional = true } -types-requests = { version = ">=0.1", optional = true } -types-setuptools = { version = ">=0.1", optional = true } -vcrpy = { version = ">=6.0.1", optional = true } - -# Docs -jupyterlab = { version = ">=3", optional = true } -ipywidgets = { version = ">=7.7.0", optional = true } -widgetsnbextension = { version = ">=3.6.0", optional = true } -# Prevent install of 1.6.0 because the module mkdocs.tests -# is no longer exported, which causes mkdocs-jupyter to -# break with a ModuleNotFoundError. -mkdocs = { version = ">=1.2,!=1.6.0", optional = true } -mkdocs-material = { version = ">=7.1,<10.0", optional = true } -mkdocs-redirects = { version = ">=1.2.1", optional = true } -markdown-callouts = { version = ">=0.2.0", optional = true } -markdown-include = { version = ">=0.6", optional = true } -mkdocstrings = {extras = ["python"], version = ">=0.19.0", optional = true} -mkdocs-jupyter = { version = ">=0.19.0", optional = true } -pymdown-extensions = { version = ">=9.2", optional = true } -pygments = { version = ">=2.11.1", optional = true } -# for notebook integrations and documentation examples -xarray = { version = ">=2023.01", optional = true } -matplotlib = { version = ">=3.3", optional = true } -h5netcdf = { version = ">=0.11", optional = true } -pyproj = [ - { version = ">=3.5.0", python = "<3.12", optional = true }, - { version = ">=3.6.1", python = ">=3.12", optional = true }, +test = [ + "mypy >=0.812", + "pytest >=6.0", + "pytest-cov >=2.8", + "pytest-watch >=4.2", + "python-magic >=0.4", + "responses >=0.14", + "types-requests >=0.1", + "types-setuptools >=0.1", + "vcrpy >=6.0.1", ] -# The following error occurs when building the docs, so we must explicitly -# include lxml-html-clean as a dev dependency until mkdocs-jupyter is updated: -# -# ImportError: lxml.html.clean module is now a separate project lxml_html_clean. -# Install lxml[html_clean] or lxml_html_clean directly. -# -# See https://github.com/danielfrg/mkdocs-jupyter/issues/200 -# See https://github.com/danielfrg/mkdocs-jupyter/issues/197 -lxml-html-clean = {version = ">=0.1.1", optional = true} - -[tool.poetry.extras] -kerchunk = ["kerchunk", "dask"] -dev = ["bump-my-version", "pre-commit", "ruff"] -test = ["mypy", "pytest", "pytest-cov", "pytest-watch", "python-magic", "responses", "types-requests", "types-setuptools", "vcrpy"] docs = [ - "jupyterlab", - "mkdocs", - "mkdocs-material", - "mkdocs-redirects", - "markdown-callouts", - "markdown-include", - "mkdocstrings", - "mkdocs-jupyter", - "pymdown-extensions", - "ipywidgets", - "widgetsnbextension", - "xarray", - "matplotlib", - "h5netcdf", - "pyproj", + "jupyterlab >=3", + "ipywidgets >=7.7.0", + "widgetsnbextension >=3.6.0", + # Prevent install of 1.6.0 because the module mkdocs.tests + # is no longer exported, which causes mkdocs-jupyter to + # break with a ModuleNotFoundError. + # for notebook integrations and documentation examples + "mkdocs >=1.2,!=1.6.0", + "mkdocs-material >=7.1,<10.0", + "mkdocs-redirects >=1.2.1", + "markdown-callouts >=0.2.0", + "markdown-include >=0.6", + "mkdocs-jupyter >=0.19.0", + "mkdocstrings[python] >=0.19.0", + "pymdown-extensions >=9.2", + "pygments >=2.11.1", + "xarray >=2023.01", + "matplotlib >=3.3", + "h5netcdf >=0.11", + "pyproj >=3.5.0;python<3.12", + "pyproj >=3.6.1;python>=3.12", + # The following error occurs when building the docs, so we must explicitly + # include lxml-html-clean as a dev dependency until mkdocs-jupyter is updated: + # + # ImportError: lxml.html.clean module is now a separate project lxml_html_clean. + # Install lxml[html_clean] or lxml_html_clean directly. + # + # See https://github.com/danielfrg/mkdocs-jupyter/issues/200 + # See https://github.com/danielfrg/mkdocs-jupyter/issues/197 + "lxml-html-clean >=0.1.1", ] -[tool.poetry.group.dev.dependencies] [build-system] requires = ["poetry-core>=1.0.0"] From edd6442b16646835b67964c56b418e5bbfe54c09 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 7 Sep 2024 10:01:59 -0600 Subject: [PATCH 10/38] Replace caret dependency notation --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 975f7a4b..d0977ab5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,7 +42,7 @@ dependencies = [ "requests >=2.26", "s3fs >=2022.11", "fsspec >=2022.11", - "tinynetrc ^1.3.1", + "tinynetrc >=1.3.1", "multimethod >=1.8", "importlib-resources >=6.3.2", "typing_extensions >=4.10.0", From 6ac66b7179c05605d7f2869906957ff1717ca48c Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 7 Sep 2024 10:11:46 -0600 Subject: [PATCH 11/38] Fixup conditional dependency specifications --- pyproject.toml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index d0977ab5..0be536e6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -46,8 +46,8 @@ dependencies = [ "multimethod >=1.8", "importlib-resources >=6.3.2", "typing_extensions >=4.10.0", - "numpy >=1.24.0;python<3.12", - "numpy >=1.26.0;python>=3.12", + "numpy >=1.24.0; python_version < '3.12'", + "numpy >=1.26.0; python_version >= '3.12'", ] ## Optional dependencies; can be opted-in with extra specifications below @@ -97,8 +97,8 @@ docs = [ "xarray >=2023.01", "matplotlib >=3.3", "h5netcdf >=0.11", - "pyproj >=3.5.0;python<3.12", - "pyproj >=3.6.1;python>=3.12", + "pyproj >=3.5.0; python_version < '3.12'", + "pyproj >=3.6.1; python_version >= '3.12'", # The following error occurs when building the docs, so we must explicitly # include lxml-html-clean as a dev dependency until mkdocs-jupyter is updated: # From a39a519974136ffb8502f7debe654ee12ef41f85 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 7 Sep 2024 10:26:42 -0600 Subject: [PATCH 12/38] Unpin kerchunk extra dependencies This probably never worked? Kerchunk doesn't use calver. --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 0be536e6..2a0ddf7e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,8 +58,8 @@ dependencies = [ # kerchunk requires numpy, but numpy >=1.26.0 is required for Python 3.12 support [project.optional-dependencies] kerchunk = [ - "kerchunk >=2022.1.0", - "dask >=0.1.2", + "kerchunk", + "dask", ] dev = [ "bump-my-version >=0.10.0", From 4c573063ab473254d9450c7c2ebfd13586e033f4 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 7 Sep 2024 09:30:46 -0600 Subject: [PATCH 13/38] Remove poetry - Replace Poetry - For dev, use `pip` & `venv` (users can of course use anything else that's standards-compliant, like `uv`) - For calculating minimum dependencies and reproducible locking, use `uv` - For build, use hatchling - Document usage of `pip` and `venv` in developer documentation. - Remove Makefile -- it's undocumented anyway! - Add Nox for task-running - Remove redundant scripts - Linting is run with pre-commit - Type checking is run with Nox - Update CI - Publish with PyPA official action --- .github/workflows/publish.yml | 27 +- .pre-commit-config.yaml | 9 +- Makefile | 48 - docs/contributing/development.md | 76 +- noxfile.py | 36 + poetry.lock | 5270 ------------------------------ pyproject.toml | 36 +- scripts/lint.sh | 5 - scripts/publish.sh | 7 - scripts/typecheck.sh | 5 - uv.lock | 4235 ++++++++++++++++++++++++ 11 files changed, 4345 insertions(+), 5409 deletions(-) delete mode 100644 Makefile create mode 100644 noxfile.py delete mode 100644 poetry.lock delete mode 100755 scripts/lint.sh delete mode 100755 scripts/publish.sh delete mode 100644 scripts/typecheck.sh create mode 100644 uv.lock diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 12f158cb..9d9acd42 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -5,13 +5,32 @@ on: jobs: build: + name: Build package runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 + - name: verify version matches git tag run: scripts/verify_tag.sh - - name: Build and publish to pypi - uses: JRubics/poetry-publish@v2.0 + + - uses: hynek/build-and-inspect-python-package@v2 + + publish: + name: Publish to PyPI + needs: ["build"] + runs-on: ubuntu-latest + environment: pypi + permissions: + id-token: write + steps: + - uses: actions/download-artifact@v4 + with: + name: Packages + path: dist + + - uses: pypa/gh-action-pypi-publish@release/v1 + # NOTE: This is not the current best practice. Instead, we should use + # "trusted publishing": + # https://github.com/pypa/gh-action-pypi-publish?tab=readme-ov-file#trusted-publishing with: - python_version: "3.9" - pypi_token: ${{ secrets.PYPI_TOKEN }} + password: ${{ secrets.PYPI_TOKEN }} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index e9fbe175..6cb5d1a2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -27,20 +27,13 @@ repos: - id: no-commit-to-branch # protects `main` by default - id: trailing-whitespace - - repo: https://github.com/python-poetry/poetry - rev: '1.8.3' - hooks: - - id: poetry-check - # This hook is very slow! Run with `pre-commit run -a poetry-lock --hook-stage manual` - - id: poetry-lock - stages: [manual] - - repo: https://github.com/astral-sh/ruff-pre-commit rev: v0.6.3 hooks: - id: ruff args: ["--fix", "--exit-non-zero-on-fix"] - id: ruff-format + - repo: https://github.com/google/yamlfmt rev: v0.13.0 hooks: diff --git a/Makefile b/Makefile deleted file mode 100644 index d8299399..00000000 --- a/Makefile +++ /dev/null @@ -1,48 +0,0 @@ -.PHONY: help - -# Shell that make should use -SHELL:=bash - -# Capture git branch and hash information -# https://stackoverflow.com/questions/43008842/capture-git-branch-name-in-makefile-variable -BRANCH := $(shell git rev-parse --abbrev-ref HEAD) -HASH := $(shell git rev-parse HEAD) - -# - to suppress if it doesn't exist --include make.env - -help: -# http://marmelab.com/blog/2016/02/29/auto-documented-makefile.html -# adds anything that has a double # comment to the phony help list - @grep -E '^[0-9a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ".:*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' - -python-three-eight: ## setup python3.8 virtual environment using poetry - poetry env use python3.8 - PIP_REQUIRE_VENV=0 poetry install - -python-three-nine: ## setup python3.9 virtual environment using poetry - poetry env use python3.9 - PIP_REQUIRE_VENV=0 poetry install - -python-three-ten: ## setup python3.10 virtual environment using poetry - poetry env use python3.10 - PIP_REQUIRE_VENV=0 poetry install - -pre-commit: ## setup pre-commit within poetry - poetry run pre-commit install - -lint: ## lint the code - bash scripts/lint.sh - -format: ## format the code - bash scripts/format.sh - -test: ## lint the code - bash scripts/test.sh - -docs-live: ## make live docs - bash scripts/docs-live.sh - -install: ## uninstall and install package with python - poetry remove ./earthaccess - poetry add ./earthaccess diff --git a/docs/contributing/development.md b/docs/contributing/development.md index 0350329f..f895e62b 100644 --- a/docs/contributing/development.md +++ b/docs/contributing/development.md @@ -1,62 +1,54 @@ -# Development environment setup +# Development + +## Getting the code 1. Fork [nsidc/earthaccess](https://github.com/nsidc/earthaccess) 1. Clone your fork (`git clone git@github.com:{my-username}/earthaccess`) -`earthaccess` uses Poetry to build and publish the package to PyPI, the defacto Python repository. In order to develop new features or fix bugs etc. we need to set up a virtual environment and install the library locally. We can accomplish this with Conda and Poetry, or just with Poetry. Both workflows achieve the same result. +In order to develop new features or fix bugs etc. we need to set up a virtual +environment and install the library locally. -### Using Conda +## Quickstart development -If we have `mamba` (or `conda`) installed, we can use the environment file included in the `ci` folder. This will install all the libraries we need (including Poetry) to start developing `earthaccess`: +The fastest way to start with development is to use nox. If you don't have nox, +you can use `pipx run nox` to run it without installing, or `pipx install nox`. +If you don't have pipx (pip for applications), then you can install with +`pip install pipx` (the only case were installing an application with regular +pip is reasonable). If you use macOS, then pipx and nox are both in brew, use +`brew install pipx nox`. -```bash -mamba env update -f ci/environment-dev.yml -mamba activate earthaccess-dev -poetry install +To use, run `nox`. This will typecheck and test using every installed version of +Python on your system, skipping ones that are not installed. You can also run +specific jobs: + +```console +$ nox -s typecheck # Typecheck only +$ nox -s tests # Python tests +$ nox -s build_docs -- --serve # Build and serve the docs +$ nox -s build_pkg # Make an SDist and wheel ``` -After activating our environment and installing the library with Poetry we can run Jupyter lab and start testing the local distribution or we can use `make` to run the tests and lint the code. -Now we can create a feature branch and push those changes to our fork! +Nox handles everything for you, including setting up an temporary virtual +environment for each run. -### Using Poetry +## Manual development environment setup -If we want to use Poetry, first we need to [install it](https://python-poetry.org/docs/#installation). After installing Poetry we can use the same workflow we used for Conda, first we install the library locally: +Create and activate a virtual environment with `venv`, which comes by default with +Python, in the `.venv` directory: ```bash -poetry install +python -m venv .venv +. .venv/bin/activate ``` -and now we can run the local Jupyter Lab and run the scripts etc. using Poetry: +Install _earthaccess_ in editable mode with optional development dependencies: ```bash -poetry run jupyter lab +pip install --editable .[dev,test,docs] ``` -!!! note - - You may need to use `poetry run make ...` to run commands in the environment. - -### Managing Dependencies - -If you need to add a new dependency, you should do the following: - -- Run `poetry add ` for a required (non-development) dependency -- Run `poetry add --group=dev ` for a development dependency, such - as a testing or code analysis dependency - -Both commands add an entry to `pyproject.toml` with a version that is -compatible with the rest of the dependencies. However, `poetry` pins versions -with a caret (`^`), which is not what we want. Therefore, you must locate the -new entry in `pyproject.toml` and change the `^` to `>=`. (See -[poetry-relax](https://github.com/zanieb/poetry-relax) for the reasoning behind -this.) - -In addition, you must also add a corresponding entry to -`ci/environment-mindeps.yaml`. You'll notice in this file that required -dependencies should be pinned exactly to the versions specified in -`pyproject.toml` (after changing `^` to `>=` there), and that development -dependencies should be left unpinned. +## Managing Dependencies -Finally, for _development dependencies only_, you must add an entry to -`ci/environment-dev.yaml` with the same version constraint as in -`pyproject.toml`. +If you need to add a new dependency, edit `pyproject.toml` and insert the dependency in +the correct location (either in the `dependencies` array or +`[project.optional-dependencies]`. diff --git a/noxfile.py b/noxfile.py new file mode 100644 index 00000000..882ffb33 --- /dev/null +++ b/noxfile.py @@ -0,0 +1,36 @@ +from __future__ import annotations + +import shutil +from pathlib import Path + +import nox + +DIR = Path(__file__).parent.resolve() + +nox.needs_version = ">=2024.3.2" +nox.options.sessions = ["typecheck", "test"] +nox.options.default_venv_backend = "uv|virtualenv" + + +@nox.session +def typecheck(session: nox.Session) -> None: + session.install("--editable", ".[test]") + session.run("mypy", ".") + + +@nox.session +def test_unit(session: nox.Session) -> None: + """Run the unit tests.""" + session.install("--editable", ".[test]") + session.run("pytest", "tests/unit", *session.posargs) + + +@nox.session +def build_pkg(session: nox.Session) -> None: + """Build a source distribution and binary distribution (wheel).""" + build_path = DIR.joinpath("build") + if build_path.exists(): + shutil.rmtree(build_path) + + session.install("build") + session.run("python", "-m", "build") diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 0935fff0..00000000 --- a/poetry.lock +++ /dev/null @@ -1,5270 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. - 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"Luis Lopez ", - "Joseph H. Kennedy ", - "James Bourbeau ", - "Matt Fisher ", - "Chuck Daniels " + {name = "Luis Lopez", email = "betolin@gmail.com"}, + {name = "Joseph H. Kennedy", email = "jhkennedy@alaska.edu"}, + {name = "James Bourbeau", email = "james@coiled.io"}, + {name = "Matt Fisher", email = "mfisher87@gmail.com"}, + {name = "Chuck Daniels", email = "chuck@developmentseed.org"}, ] license = "MIT" readme = "README.md" @@ -33,9 +35,6 @@ classifiers = [ requires-python = ">=3.9" -# NOTE: Minimum dependencies are tested with the packages defined in the -# `ci/environment-mindeps.yaml` conda environment. When updating minimum dependencies -# here, make sure to also update `ci/environment-mindeps.yaml`. dependencies = [ "python-cmr >=0.10.0", "pqdm >=0.1", @@ -46,16 +45,12 @@ dependencies = [ "multimethod >=1.8", "importlib-resources >=6.3.2", "typing_extensions >=4.10.0", + # kerchunk requires numpy, but numpy >=1.26.0 is required for Python 3.12 + # support "numpy >=1.24.0; python_version < '3.12'", "numpy >=1.26.0; python_version >= '3.12'", ] -## Optional dependencies; can be opted-in with extra specifications below -## This is so verbose because Poetry requires it: https://python-poetry.org/docs/pyproject#extras -## If we switch to PEP621 specification, we can specify extras (called -## "optional" under PEP621) with versions in one line: -#https://peps.python.org/pep-0621/#example -# kerchunk requires numpy, but numpy >=1.26.0 is required for Python 3.12 support [project.optional-dependencies] kerchunk = [ "kerchunk", @@ -64,7 +59,8 @@ kerchunk = [ dev = [ "bump-my-version >=0.10.0", "pre-commit >=2.4", - "ruff >=0.4.2", + "ruff >=0.6.3", + "uv >=0.4.7", ] test = [ "mypy >=0.812", @@ -112,8 +108,8 @@ docs = [ [build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +requires = ["hatchling", "hatch-vcs"] +build-backend = "hatchling.build" [tool.pytest] filterwarnings = ["error::UserWarning"] @@ -192,5 +188,5 @@ search = 'date-released: "\d{{4}}-\d{{2}}-\d{{2}}"' replace = 'date-released: "{now:%Y-%m-%d}"' [tool.codespell] -skip = 'poetry.lock,*.ipynb,*.yml,*.yaml,./tests' +skip = 'uv.lock,*.ipynb,*.yml,*.yaml,./tests' ignore-words = ".codespellignore" diff --git a/scripts/lint.sh b/scripts/lint.sh deleted file mode 100755 index 61324ea6..00000000 --- a/scripts/lint.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/usr/bin/env bash - -set -ex - -ruff check . diff --git a/scripts/publish.sh b/scripts/publish.sh deleted file mode 100755 index aa459c10..00000000 --- a/scripts/publish.sh +++ /dev/null @@ -1,7 +0,0 @@ -#!/usr/bin/env bash 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insertions(+), 55 deletions(-) delete mode 100644 ci/environment-mindeps.yaml delete mode 100755 scripts/test.sh diff --git a/.github/workflows/test-mindeps.yml b/.github/workflows/test-mindeps.yml index e432280a..362c9d7a 100644 --- a/.github/workflows/test-mindeps.yml +++ b/.github/workflows/test-mindeps.yml @@ -1,4 +1,4 @@ -name: Test minimum dependencies +name: Unit test minimum dependencies on: push: @@ -11,11 +11,6 @@ concurrency: group: test-mindeps-${{ github.ref }} cancel-in-progress: true -# Required shell entrypoint to have properly activated conda environments -defaults: - run: - shell: bash -l {0} - jobs: test-mindeps: runs-on: ubuntu-latest @@ -25,25 +20,26 @@ jobs: steps: - name: Checkout source uses: actions/checkout@v4.1.1 - - name: Setup Conda Environment - uses: conda-incubator/setup-miniconda@v3.0.4 + + - name: Install uv + uses: astral-sh/setup-uv@v2 + with: + version: "0.4.7" + enable-cache: true + + - name: Set up Python + uses: actions/setup-python@v5 with: - miniforge-variant: Mambaforge - miniforge-version: latest - use-mamba: true - channel-priority: strict - environment-file: ci/environment-mindeps.yaml - activate-environment: test-environment - auto-activate-base: false + python-version-file: pyproject.toml - - name: Install - run: python -m pip install --no-deps -e . + - name: Install minimum-compatible dependencies + run: uv sync --resolution lowest-direct - - name: mamba list - run: mamba list + - name: Install earthaccess + run: uv pip install --no-deps . - name: Test - run: bash scripts/test.sh + run: pytest tests/unit --cov=earthaccess --cov=tests --cov-report=term-missing --capture=no --tb=native --log-cli-level=INFO - name: Upload coverage # Don't upload coverage when using the `act` tool to run the workflow locally diff --git a/ci/environment-mindeps.yaml b/ci/environment-mindeps.yaml deleted file mode 100644 index 76f81434..00000000 --- a/ci/environment-mindeps.yaml +++ /dev/null @@ -1,29 +0,0 @@ -# NOTE: Minimum dependencies are defined in `pyproject.toml`. -# This file is only used for testing purposes. -# When making changes to minimum dependencies, make sure both this file -# and `pyproject.toml` are consistent with each other. -name: test-environment -channels: - - conda-forge -dependencies: - # required dependencies - - python=3.9 - - python-cmr=0.10.0 - - pqdm=0.1 - - requests=2.26 - - s3fs=2022.11 - - fsspec=2022.11 - - tinynetrc=1.3.1 - - multimethod=1.8 - - importlib-resources=6.3.2 - - typing-extensions=4.10.0 - # test dependencies - - responses - - pytest - - pytest-cov - - python-magic - - mypy - - types-requests - - types-setuptools - - ruff - - vcrpy diff --git a/scripts/test.sh b/scripts/test.sh deleted file mode 100755 index 1c74c349..00000000 --- a/scripts/test.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env bash - -set -e -set -x - -pytest tests/unit --cov=earthaccess --cov=tests --cov-report=term-missing "${@}" -s --tb=native --log-cli-level=INFO From 5f5986fae12e0cc36b0497df7378d54e4811bbfa Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 7 Sep 2024 11:34:18 -0600 Subject: [PATCH 15/38] Encode mypy's files and python version in config --- pyproject.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 94b0d1e6..193739ee 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -115,6 +115,8 @@ build-backend = "hatchling.build" filterwarnings = ["error::UserWarning"] [tool.mypy] +python_version = "3.9" +files = ["earthaccess", "tests"] mypy_path = ["earthaccess", "tests", "stubs"] disallow_untyped_defs = true # TODO: incrementally work towards strict mode (currently too many errors) From 6dada1a339affb7bfdba25fad80138fbdb7fbd78 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 7 Sep 2024 11:37:02 -0600 Subject: [PATCH 16/38] Replace poetry in GitHub Actions --- .github/actions/install-pkg/action.yml | 23 ++++++++++++++ .github/workflows/integration-test.yml | 41 ++++--------------------- .github/workflows/test.yml | 42 +++++--------------------- scripts/integration-test.sh | 2 -- 4 files changed, 36 insertions(+), 72 deletions(-) create mode 100644 .github/actions/install-pkg/action.yml diff --git a/.github/actions/install-pkg/action.yml b/.github/actions/install-pkg/action.yml new file mode 100644 index 00000000..195466aa --- /dev/null +++ b/.github/actions/install-pkg/action.yml @@ -0,0 +1,23 @@ +name: Install earthaccess Python package +description: Install earthaccess Python package and testing dependencies' + +inputs: + python-version: + required: true + +runs: + using: composite + steps: + - uses: actions/setup-python@v5 + with: + python-version: ${{ inputs.python-version }} + cache: pip + + - name: Display full python version + id: full-python-version + run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))") + + - name: Install package and test dependencies + shell: bash + run: | + pip install .[test] diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index b5eead1d..d20fa9fe 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -17,58 +17,29 @@ concurrency: group: integration-tests-${{ github.ref }} cancel-in-progress: true -defaults: - run: - shell: bash -l {0} - jobs: integration-tests: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.9", "3.12"] fail-fast: false steps: - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 + + - uses: ./.github/actions/install-pkg with: python-version: ${{ matrix.python-version }} - - name: Get full python version - id: full-python-version - run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))") - - name: Install poetry - uses: abatilo/actions-poetry@v3 - - name: Configure poetry - run: | - poetry config virtualenvs.create true --local - poetry config virtualenvs.in-project true --local - poetry self add setuptools - - name: Set up cache - uses: actions/cache@v4 - id: cache - with: - path: .venv - key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('poetry.lock') }} - - name: Ensure cache is healthy - if: steps.cache.outputs.cache-hit == 'true' - run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv - - name: Install dependencies - if: ${{ !env.ACT }} - run: poetry install -E test - - name: Install dependencies - if: ${{ env.ACT }} - # When using `act` to run the workflow locally, the `poetry install` command - # may fail due to network issues when running multiple Docker containers. - run: poetry install -E test || poetry install -E test || poetry install -E test + - name: Test env: EARTHDATA_USERNAME: ${{ secrets.EDL_USERNAME }} EARTHDATA_PASSWORD: ${{ secrets.EDL_PASSWORD }} EARTHACCESS_TEST_USERNAME: ${{ secrets.EDL_USERNAME }} EARTHACCESS_TEST_PASSWORD: ${{ secrets.EDL_PASSWORD }} - run: poetry run bash scripts/integration-test.sh + run: ./scripts/integration-test.sh + - name: Upload coverage # Don't upload coverage when using the `act` tool to run the workflow locally if: ${{ !env.ACT }} diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 7f81e00a..af5fd1f6 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -7,10 +7,6 @@ on: pull_request: types: [opened, synchronize] -defaults: - run: - shell: bash -l {0} - jobs: unit-tests: runs-on: ubuntu-latest @@ -21,41 +17,17 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 + + - uses: ./.github/actions/install-pkg with: python-version: ${{ matrix.python-version }} - - name: Get full python version - id: full-python-version - run: echo "version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")" >> $GITHUB_OUTPUT - - name: Install poetry - uses: abatilo/actions-poetry@v3 - - name: Configure poetry - run: | - poetry config virtualenvs.create true --local - poetry config virtualenvs.in-project true --local - poetry self add setuptools - - name: Set up cache - uses: actions/cache@v4 - id: cache - with: - path: .venv - key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('poetry.lock') }} - - name: Ensure cache is healthy - if: steps.cache.outputs.cache-hit == 'true' - run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv - - name: Install dependencies - if: ${{ !env.ACT }} - run: poetry install -E test - - name: Install dependencies - if: ${{ env.ACT }} - # When using `act` to run the workflow locally, the `poetry install` command - # may fail due to network issues when running multiple Docker containers. - run: poetry install -E test || poetry install -E test || poetry install -E test + - name: Typecheck - run: poetry run bash scripts/typecheck.sh + run: mypy + - name: Test - run: poetry run bash scripts/test.sh + run: pytest tests/unit --cov=earthaccess --cov=tests --cov-report=term-missing --capture=no --tb=native --log-cli-level=INFO + - name: Upload coverage # Don't upload coverage when using the `act` tool to run the workflow locally if: ${{ !env.ACT }} diff --git a/scripts/integration-test.sh b/scripts/integration-test.sh index 7a7b6551..15b173f8 100755 --- a/scripts/integration-test.sh +++ b/scripts/integration-test.sh @@ -14,5 +14,3 @@ if [[ $RET == 99 ]]; then elif [[ $RET != 0 ]]; then exit $RET fi - -bash ./scripts/lint.sh From 8e8a7e78365123eaffcdb9b5cb22ad184abe2251 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 7 Sep 2024 11:39:28 -0600 Subject: [PATCH 17/38] Replace poetry in conda dev environment --- ci/environment-dev.yml | 21 +++------------------ 1 file changed, 3 insertions(+), 18 deletions(-) diff --git a/ci/environment-dev.yml b/ci/environment-dev.yml index 60ebcac8..3eb3df8b 100644 --- a/ci/environment-dev.yml +++ b/ci/environment-dev.yml @@ -2,25 +2,10 @@ name: earthaccess-dev channels: - conda-forge dependencies: - # This environment bootstraps poetry, the actual dev environment - # is installed and managed with poetry + # This environment bootstraps pip, the actual dev environment + # is installed and managed with pip - python=3.10 - - jupyterlab=3 - - xarray>=0.19 - - ipyleaflet>=0.13 - - h5netcdf>=0.11 - - cartopy - - - mkdocs>=1.2 - - mkdocs-material>=7.1,<9.0 - - markdown-include>=0.6 - - mkdocs-redirects>=1.2.1 - - mkdocstrings>=0.19.0 - - mkdocstrings-python - - mkdocs-jupyter>=0.19.0 - - pymdown-extensions>=9.2 - pip - pip: - - poetry - - markdown-callouts>=0.2.0 + - --editable .[dev] From 8643011ec4b7da3ee1dda3291ec89f348d19f498 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 7 Sep 2024 11:43:49 -0600 Subject: [PATCH 18/38] Replace poetry for binder --- binder/environment.yml | 4 ++++ binder/postBuild | 6 ------ 2 files changed, 4 insertions(+), 6 deletions(-) delete mode 100755 binder/postBuild diff --git a/binder/environment.yml b/binder/environment.yml index 2bc59969..95c0496b 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -18,3 +18,7 @@ dependencies: - hvplot - holoviews - panel + + - pip + - pip: + - "." diff --git a/binder/postBuild b/binder/postBuild deleted file mode 100755 index bcf7589f..00000000 --- a/binder/postBuild +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/bash -# -set -ex - -poetry config virtualenvs.create false -poetry install --no-dev From bd3fe744224694984bcdaeb65de2a0eff9e0445b Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 7 Sep 2024 11:48:52 -0600 Subject: [PATCH 19/38] Replace poetry for readthedocs --- readthedocs.yml | 24 ++++++------------------ 1 file changed, 6 insertions(+), 18 deletions(-) diff --git a/readthedocs.yml b/readthedocs.yml index 12df42af..5e44b0d9 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -10,24 +10,12 @@ build: os: ubuntu-22.04 tools: python: "3.10" - jobs: - post_create_environment: - # Install poetry - - asdf plugin add poetry - # HACK: As of ~2024-05-07, poetry "latest" is not installable with - # asdf ("Version 1.8.3 does not exist") because the latest tagged version - # of poetry is not yet released. Should we avoid using "latest" from here - # on, or change it back once 1.8.3 is released? - - asdf install poetry 1.8.2 - - asdf global poetry 1.8.2 - # Tell poetry to not use a virtual environment - - poetry config virtualenvs.create false - post_install: - # Install dependencies with 'docs' dependency group - # https://python-poetry.org/docs/managing-dependencies/#dependency-groups - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install -E docs - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry env info - - pip freeze mkdocs: configuration: mkdocs.yml + +python: + install: + - path: "." + extra_requirements: + - docs From cadcbddde500c2b1c93c4a23a1482b35f0145cfb Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 7 Sep 2024 11:52:01 -0600 Subject: [PATCH 20/38] Add nox dev dependency and fixup noxfile --- noxfile.py | 5 +++-- pyproject.toml | 1 + 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/noxfile.py b/noxfile.py index 882ffb33..cadc109d 100644 --- a/noxfile.py +++ b/noxfile.py @@ -8,14 +8,15 @@ DIR = Path(__file__).parent.resolve() nox.needs_version = ">=2024.3.2" -nox.options.sessions = ["typecheck", "test"] +nox.options.sessions = ["typecheck", "test_unit"] nox.options.default_venv_backend = "uv|virtualenv" @nox.session def typecheck(session: nox.Session) -> None: + """Typecheck with mypy.""" session.install("--editable", ".[test]") - session.run("mypy", ".") + session.run("mypy") @nox.session diff --git a/pyproject.toml b/pyproject.toml index 193739ee..a816d2b7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,6 +58,7 @@ kerchunk = [ ] dev = [ "bump-my-version >=0.10.0", + "nox", "pre-commit >=2.4", "ruff >=0.6.3", "uv >=0.4.7", From e194f14f321d8146331478d50cfaf0de077c2e89 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 7 Sep 2024 12:03:58 -0600 Subject: [PATCH 21/38] Fixup composable action --- .github/actions/install-pkg/action.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/actions/install-pkg/action.yml b/.github/actions/install-pkg/action.yml index 195466aa..37538229 100644 --- a/.github/actions/install-pkg/action.yml +++ b/.github/actions/install-pkg/action.yml @@ -14,10 +14,10 @@ runs: cache: pip - name: Display full python version + shell: bash id: full-python-version run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))") - name: Install package and test dependencies shell: bash - run: | - pip install .[test] + run: pip install .[test] From c0cf028c0776e857dd5d7c41e1247f4ee85b4e8a Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 7 Sep 2024 12:05:31 -0600 Subject: [PATCH 22/38] Install test deps for mindeps test action --- .github/workflows/test-mindeps.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-mindeps.yml b/.github/workflows/test-mindeps.yml index 362c9d7a..3be5bb01 100644 --- a/.github/workflows/test-mindeps.yml +++ b/.github/workflows/test-mindeps.yml @@ -33,13 +33,13 @@ jobs: python-version-file: pyproject.toml - name: Install minimum-compatible dependencies - run: uv sync --resolution lowest-direct + run: uv sync --resolution lowest-direct --extra test - name: Install earthaccess run: uv pip install --no-deps . - name: Test - run: pytest tests/unit --cov=earthaccess --cov=tests --cov-report=term-missing --capture=no --tb=native --log-cli-level=INFO + run: uv run pytest tests/unit --cov=earthaccess --cov=tests --cov-report=term-missing --capture=no --tb=native --log-cli-level=INFO - 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id: ruff-format + - repo: https://github.com/astral-sh/uv-pre-commit + rev: "0.4.7" + hooks: + - id: uv-lock + - repo: https://github.com/google/yamlfmt rev: v0.13.0 hooks: diff --git a/uv.lock b/uv.lock index b3baa22b..e4c8a627 100644 --- a/uv.lock +++ b/uv.lock @@ -909,8 +909,8 @@ requires-dist = [ { name = "pymdown-extensions", marker = "extra == 'docs'", specifier = ">=9.2" }, { name = "pyproj", marker = "python_full_version >= '3.12' and extra == 'docs'", specifier = ">=3.6.1" }, { name = "pyproj", marker = "python_full_version < '3.12' and extra == 'docs'", specifier = ">=3.5.0" }, - { name = "pytest", marker = "extra == 'test'", specifier = ">=6.0" }, - { name = "pytest-cov", marker = "extra == 'test'", specifier = ">=2.8" }, + { name = "pytest", marker = "extra == 'test'", specifier = ">=8.3" }, + { name = "pytest-cov", marker = "extra == 'test'", specifier = ">=5.0" }, { name = "pytest-watch", marker = "extra == 'test'", specifier = ">=4.2" }, { name = "python-cmr", specifier = ">=0.10.0" }, { name = "python-magic", marker = "extra == 'test'", specifier = ">=0.4" }, From 4409b1123b9cc017f0526993e3f511b3971dc499 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Wed, 11 Sep 2024 10:40:48 -0600 Subject: [PATCH 25/38] Add docs dependencies to conda dev env Co-Authored-By: Luis Lopez --- ci/environment-dev.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/environment-dev.yml b/ci/environment-dev.yml index 3eb3df8b..68f13db4 100644 --- a/ci/environment-dev.yml +++ b/ci/environment-dev.yml @@ -8,4 +8,4 @@ dependencies: - pip - pip: - - --editable .[dev] + - --editable .[dev,docs] From bff4354295c918e59377bcbf852dba913d81dea9 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Wed, 11 Sep 2024 10:45:12 -0600 Subject: [PATCH 26/38] Restore integration tests to run on all supported Python versions Co-Authored-By: Luis Lopez --- .github/workflows/integration-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index d20fa9fe..cb013525 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -22,7 +22,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.9", "3.12"] + python-version: ["3.9", "3.10", "3.11", "3.12"] fail-fast: false steps: From adbc43caf891fb93856d8bde992ffb0666a55f95 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Wed, 11 Sep 2024 11:05:35 -0600 Subject: [PATCH 27/38] Move dev environment file out of CI directory --- ci/environment-dev.yml => environment-dev.yml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename ci/environment-dev.yml => environment-dev.yml (100%) diff --git a/ci/environment-dev.yml b/environment-dev.yml similarity index 100% rename from ci/environment-dev.yml rename to environment-dev.yml From 82381d74ff3ca8a197fca1755a96298ddadbfb46 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 14 Sep 2024 11:12:24 -0600 Subject: [PATCH 28/38] Fix typo Co-authored-by: Chuck Daniels --- .github/actions/install-pkg/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/actions/install-pkg/action.yml b/.github/actions/install-pkg/action.yml index 37538229..0b292180 100644 --- a/.github/actions/install-pkg/action.yml +++ b/.github/actions/install-pkg/action.yml @@ -1,5 +1,5 @@ name: Install earthaccess Python package -description: Install earthaccess Python package and testing dependencies' +description: Install earthaccess Python package and testing dependencies inputs: python-version: From 87c22ea7274cc52afdc66114a46fe9e46b999717 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 14 Sep 2024 11:13:24 -0600 Subject: [PATCH 29/38] Use modern syntax to get Actions output into GUI Co-authored-by: Chuck Daniels --- .github/actions/install-pkg/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/actions/install-pkg/action.yml b/.github/actions/install-pkg/action.yml index 0b292180..af1ebfe7 100644 --- a/.github/actions/install-pkg/action.yml +++ b/.github/actions/install-pkg/action.yml @@ -16,7 +16,7 @@ runs: - name: Display full python version shell: bash id: full-python-version - run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))") + run: echo "{version}=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")" >> $GITHUB_OUTPUT - name: Install package and test dependencies shell: bash From c5c414e26d87680d58ead4b7876483d891dc2d19 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 14 Sep 2024 11:13:46 -0600 Subject: [PATCH 30/38] Fix spelling Co-authored-by: Chuck Daniels --- docs/contributing/development.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/contributing/development.md b/docs/contributing/development.md index f895e62b..fd5c0fc8 100644 --- a/docs/contributing/development.md +++ b/docs/contributing/development.md @@ -28,7 +28,7 @@ $ nox -s build_docs -- --serve # Build and serve the docs $ nox -s build_pkg # Make an SDist and wheel ``` -Nox handles everything for you, including setting up an temporary virtual +Nox handles everything for you, including setting up a temporary virtual environment for each run. ## Manual development environment setup From f53b45168cef8ed9ac7991d293b037e696234fe2 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 14 Sep 2024 11:14:24 -0600 Subject: [PATCH 31/38] Explicitly source instead of using dot alias Co-authored-by: Chuck Daniels --- docs/contributing/development.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/contributing/development.md b/docs/contributing/development.md index fd5c0fc8..2b325d3a 100644 --- a/docs/contributing/development.md +++ b/docs/contributing/development.md @@ -38,7 +38,7 @@ Python, in the `.venv` directory: ```bash python -m venv .venv -. .venv/bin/activate +source .venv/bin/activate ``` Install _earthaccess_ in editable mode with optional development dependencies: From f96b5f0ad284eceb943fda3bcd54d621e1154eaf Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Sat, 14 Sep 2024 11:15:14 -0600 Subject: [PATCH 32/38] Clarify supported versions of Python in README Co-authored-by: Chuck Daniels --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ad7252db..2e810078 100644 --- a/README.md +++ b/README.md @@ -82,7 +82,7 @@ Visit [our quick start guide](https://earthaccess.readthedocs.io/en/latest/quick ## Compatibility -Only **Python 3.9+** is supported. +The _minimum_ supported Python version is **3.9**. ## How to Contribute to `earthaccess` From d1b619ddc78da469ae96f4a2199adfdaea4b2b70 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 17 Sep 2024 10:46:17 -0600 Subject: [PATCH 33/38] Add development guide note for conda users --- docs/contributing/development.md | 9 +++++++++ environment-dev.yml | 2 +- 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/docs/contributing/development.md b/docs/contributing/development.md index 2b325d3a..1a31a415 100644 --- a/docs/contributing/development.md +++ b/docs/contributing/development.md @@ -47,6 +47,15 @@ Install _earthaccess_ in editable mode with optional development dependencies: pip install --editable .[dev,test,docs] ``` +??? note "For conda users" + + For your convenience, there is a `environment-dev.yml` file at the root of this + repository. You can create a dev environment quickly with: + + ```bash + conda env create --file environment-dev.yml + ``` + ## Managing Dependencies If you need to add a new dependency, edit `pyproject.toml` and insert the dependency in diff --git a/environment-dev.yml b/environment-dev.yml index 68f13db4..a7a5dd01 100644 --- a/environment-dev.yml +++ b/environment-dev.yml @@ -8,4 +8,4 @@ dependencies: - pip - pip: - - --editable .[dev,docs] + - --editable .[dev,test,docs] From df578ed3635ebeab5702b9d28ddfe5c0781eb647 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 17 Sep 2024 10:50:23 -0600 Subject: [PATCH 34/38] Clarify purpose of Nox vs full dev env --- docs/contributing/development.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/contributing/development.md b/docs/contributing/development.md index 1a31a415..b5e8aeac 100644 --- a/docs/contributing/development.md +++ b/docs/contributing/development.md @@ -33,6 +33,10 @@ environment for each run. ## Manual development environment setup +While `nox` is the fastest way to get started, you may soon find that you need a full +development environment, for example to test in a REPL. This development environment +also includes `nox`. + Create and activate a virtual environment with `venv`, which comes by default with Python, in the `.venv` directory: From 0923beb6f154d9d02f23c68afa47eb5cb9ac0273 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 17 Sep 2024 10:54:56 -0600 Subject: [PATCH 35/38] Replace reference to Make --- docs/contributing/index.md | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/docs/contributing/index.md b/docs/contributing/index.md index a8b9f624..081da2df 100644 --- a/docs/contributing/index.md +++ b/docs/contributing/index.md @@ -10,11 +10,13 @@ Please note that we have a [code of conduct](./code-of-conduct.md). Please follo ## First Steps to contribute -- Read the documentation! -- Fork this repo and set up development environment (see - [development environment documentation](./development.md) for details) -- Run the unit tests successfully in `main` branch: - - `make test` +First, read the documentation! + +When you feel comfortable, fork this repository and set up your development environment. +Don't forget to run our suite of checks (see [development environment +documentation](./development.md) for details)! + +## Sharing your work with us on GitHub From here, you might want to fix and issue or bug, or add a new feature. Jump to the relevant section to proceed. From a6aee82e1d5b92e8f41bedc151e335c07c978ff5 Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 17 Sep 2024 11:45:59 -0600 Subject: [PATCH 36/38] Rename conda dev environment file --- docs/contributing/development.md | 4 ++-- environment-dev.yml => environment.yml | 0 2 files changed, 2 insertions(+), 2 deletions(-) rename environment-dev.yml => environment.yml (100%) diff --git a/docs/contributing/development.md b/docs/contributing/development.md index b5e8aeac..52e4b676 100644 --- a/docs/contributing/development.md +++ b/docs/contributing/development.md @@ -53,11 +53,11 @@ pip install --editable .[dev,test,docs] ??? note "For conda users" - For your convenience, there is a `environment-dev.yml` file at the root of this + For your convenience, there is a `environment.yml` file at the root of this repository. You can create a dev environment quickly with: ```bash - conda env create --file environment-dev.yml + conda env create --file environment.yml ``` ## Managing Dependencies diff --git a/environment-dev.yml b/environment.yml similarity index 100% rename from environment-dev.yml rename to environment.yml From 2cef7fb8279c80936853eebbdc5b99e0b71d3b0d Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 17 Sep 2024 11:46:14 -0600 Subject: [PATCH 37/38] Remove references to removed/moved files --- docs/contributing/maintainers-guide.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/docs/contributing/maintainers-guide.md b/docs/contributing/maintainers-guide.md index 2d54a354..bfbbbf47 100644 --- a/docs/contributing/maintainers-guide.md +++ b/docs/contributing/maintainers-guide.md @@ -44,11 +44,8 @@ main: This is the main branch, which is consistently tested and prepared for rel ## Continuous Integration & Delivery -The GitHub Actions CI services handle the project's building, testing, and management across Linux, macOS, and Windows platforms. The CI configuration files can be found in the `./.github/workflows/`. Here we briefly summarize the functions of the files in the `./ci/` directory. +The GitHub Actions CI services handle the project's building, testing, and management across Linux, macOS, and Windows platforms. The CI configuration files can be found in the `./.github/workflows/`. -`environment-dev.yml` - The environment configuration file specifies dependencies for Python development. - -`environment-mindeps.yaml`- Specifies an environment with the minimum supported dependency versions to detect backwards-incompatible code. ## Continuous Documentation From de313bebd4abef4f23c6436e104e9b040510f31b Mon Sep 17 00:00:00 2001 From: Matt Fisher Date: Tue, 17 Sep 2024 11:51:26 -0600 Subject: [PATCH 38/38] Move build system to top of pyproject Co-Authored-By: Joseph H Kennedy Co-authored-by: Chuck Daniels --- pyproject.toml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 1bd33c0d..f04fcb76 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,7 @@ +[build-system] +requires = ["hatchling", "hatch-vcs"] +build-backend = "hatchling.build" + [project] name = "earthaccess" version = "0.10.0" @@ -108,10 +112,6 @@ docs = [ ] -[build-system] -requires = ["hatchling", "hatch-vcs"] -build-backend = "hatchling.build" - [tool.pytest] filterwarnings = ["error::UserWarning"]