Renaming dataclasses folder, fixing linting. (#176)

* Renaming dataclasses folder. * Updating notebooks. * Relinting. * fix docs nb * fix docs nb --------- Co-authored-by: jrob93 <[email protected]>
lsst-uk · Oct 8, 2024 · ae83173 · ae83173
1 parent 769fb26
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Showing 28 changed files with 67 additions and 67 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -48,7 +48,7 @@ repos:
 
     # Analyze the code style and report code that doesn't adhere.
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 24.10.0
     hooks:
       - id: black-jupyter
         name: Format code using black

diff --git a/docs/notebooks/adler_phasecurve_example.ipynb b/docs/notebooks/adler_phasecurve_example.ipynb
@@ -16,7 +16,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid\n",
+    "from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid\n",
     "from adler.science.PhaseCurve import PhaseCurve\n",
     "\n",
     "import numpy as np\n",
@@ -351,7 +351,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/docs/notebooks/colour_functions_example.ipynb b/docs/notebooks/colour_functions_example.ipynb
@@ -17,8 +17,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid\n",
-    "from adler.dataclasses.AdlerData import AdlerData\n",
+    "from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid\n",
+    "from adler.objectdata.AdlerData import AdlerData\n",
     "from adler.science.PhaseCurve import PhaseCurve\n",
     "from adler.science.Colour import col_obs_ref\n",
     "from adler.utilities.plotting_utilities import plot_errorbar\n",
@@ -282,7 +282,7 @@
     "\n",
     "# store running colour parameters as a dataframe\n",
     "df_col = pd.DataFrame(col_dict_list)\n",
-    "df_col = pd.concat([df_obs, df_col], axis=1)\n",
+    "df_col = df_col.merge(df_obs, on=x_plot)\n",
     "\n",
     "ax1.set_xlabel(x_plot)\n",
     "ax1.set_ylabel(y_plot)\n",
@@ -361,7 +361,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "605a043a",
+   "id": "30e90de5-e50b-4339-a027-7b2165a6b664",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -383,7 +383,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.19"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

diff --git a/docs/notebooks/outlier_detection_example.ipynb b/docs/notebooks/outlier_detection_example.ipynb
@@ -16,9 +16,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid\n",
+    "from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid\n",
     "from adler.science.PhaseCurve import PhaseCurve\n",
-    "from adler.dataclasses.AdlerData import AdlerData\n",
+    "from adler.objectdata.AdlerData import AdlerData\n",
     "import adler.utilities.science_utilities as utils\n",
     "\n",
     "import numpy as np\n",
@@ -296,7 +296,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.19"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/docs/notebooks/plotting_utilities_example.ipynb b/docs/notebooks/plotting_utilities_example.ipynb
@@ -16,7 +16,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid\n",
+    "from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid\n",
     "from adler.science.PhaseCurve import PhaseCurve\n",
     "from adler.utilities.plotting_utilities import plot_errorbar\n",
     "\n",
@@ -251,7 +251,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.19"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/adler_demo/adler_demo.ipynb b/notebooks/adler_demo/adler_demo.ipynb
@@ -15,7 +15,7 @@
    },
    "outputs": [],
    "source": [
-    "from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid\n",
+    "from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid\n",
     "from adler.science.PhaseCurve import PhaseCurve\n",
     "from adler.utilities.plotting_utilities import plot_errorbar\n",
     "import adler.utilities.science_utilities as sci_utils\n",
@@ -568,9 +568,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "adler-dev",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "adler-dev"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -582,7 +582,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/adler_examples.ipynb b/notebooks/adler_examples.ipynb
@@ -7,7 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid\n",
+    "from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid\n",
     "from adler.science.PhaseCurve import PhaseCurve\n",
     "\n",
     "import numpy as np\n",
@@ -324,9 +324,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "adler-dev",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "adler-dev"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {

diff --git a/notebooks/adlerdata_in_and_out.ipynb b/notebooks/adlerdata_in_and_out.ipynb
@@ -10,8 +10,8 @@
     "import pandas as pd\n",
     "import sqlite3\n",
     "\n",
-    "from adler.dataclasses.AdlerData import AdlerData\n",
-    "from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid\n",
+    "from adler.objectdata.AdlerData import AdlerData\n",
+    "from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid\n",
     "from adler.utilities.tests_utilities import get_test_data_filepath"
    ]
   },

diff --git a/notebooks/colour_functions_demo.ipynb b/notebooks/colour_functions_demo.ipynb
@@ -27,8 +27,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid\n",
-    "from adler.dataclasses.AdlerData import AdlerData\n",
+    "from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid\n",
+    "from adler.objectdata.AdlerData import AdlerData\n",
     "from adler.science.PhaseCurve import PhaseCurve\n",
     "from adler.science.Colour import col_obs_ref\n",
     "from adler.utilities.plotting_utilities import plot_errorbar\n",
@@ -369,9 +369,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "adler-dev",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "adler-dev"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -383,7 +383,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/colour_functions_testing.ipynb b/notebooks/colour_functions_testing.ipynb
@@ -27,8 +27,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid\n",
-    "from adler.dataclasses.AdlerData import AdlerData\n",
+    "from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid\n",
+    "from adler.objectdata.AdlerData import AdlerData\n",
     "from adler.science.PhaseCurve import PhaseCurve\n",
     "from adler.science.Colour import col_obs_ref\n",
     "from adler.utilities.plotting_utilities import plot_errorbar\n",
@@ -2035,9 +2035,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "adler-dev",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "adler-dev"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -2049,7 +2049,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/outlier_detection.ipynb b/notebooks/outlier_detection.ipynb
@@ -7,9 +7,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid\n",
+    "from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid\n",
     "from adler.science.PhaseCurve import PhaseCurve\n",
-    "from adler.dataclasses.AdlerData import AdlerData\n",
+    "from adler.objectdata.AdlerData import AdlerData\n",
     "import adler.utilities.science_utilities as utils\n",
     "\n",
     "import numpy as np\n",
@@ -275,9 +275,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "adler-dev",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "adler-dev"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {

diff --git a/notebooks/plotting_utilities.ipynb b/notebooks/plotting_utilities.ipynb
@@ -27,7 +27,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid\n",
+    "from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid\n",
     "from adler.science.PhaseCurve import PhaseCurve\n",
     "from adler.utilities.plotting_utilities import plot_errorbar\n",
     "\n",
@@ -246,9 +246,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "adler-dev",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "adler-dev"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {

diff --git a/src/adler/__init__.py b/src/adler/__init__.py
@@ -1,4 +1,4 @@
-from . import dataclasses
+from . import objectdata
 from . import science
 from . import utilities
 from . import lasair
diff --git a/src/adler/adler.py b/src/adler/adler.py
@@ -7,8 +7,8 @@
 import matplotlib.gridspec as gridspec
 import os
 
-from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid
-from adler.dataclasses.AdlerData import AdlerData
+from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid
+from adler.objectdata.AdlerData import AdlerData
 from adler.science.PhaseCurve import PhaseCurve
 from adler.science.Colour import col_obs_ref
 from adler.utilities.AdlerCLIArguments import AdlerCLIArguments
@@ -102,9 +102,9 @@ def runAdler(cli_args):
                 logger.info("load previously classified observations: {}".format(save_file))
                 _df_obs = pd.read_csv(save_file, index_col=0)
                 df_obs = df_obs.merge(_df_obs, on=["diaSourceId", "midPointMjdTai"], how="left")
-                df_obs.loc[
-                    pd.isnull(df_obs["outlier_y"]), "outlier_y"
-                ] = False  # ensure that classifications exist (nan entries can only be false?). Weird behaviour here for g filter, is it to do with when new g obs appear relative to r/i etc?
+                df_obs.loc[pd.isnull(df_obs["outlier_y"]), "outlier_y"] = (
+                    False  # ensure that classifications exist (nan entries can only be false?). Weird behaviour here for g filter, is it to do with when new g obs appear relative to r/i etc?
+                )
                 df_obs = df_obs.rename({"outlier_y": "outlier"}, axis=1)
                 df_obs = df_obs.drop("outlier_x", axis=1)
             else:

diff --git a/src/adler/dataclasses/AdlerData.py → src/adler/objectdata/AdlerData.py b/src/adler/dataclasses/AdlerData.py → src/adler/objectdata/AdlerData.py
diff --git a/src/adler/dataclasses/AdlerPlanetoid.py → src/adler/objectdata/AdlerPlanetoid.py b/src/adler/dataclasses/AdlerPlanetoid.py → src/adler/objectdata/AdlerPlanetoid.py
@@ -4,11 +4,11 @@
 import logging
 import json
 
-from adler.dataclasses.Observations import Observations
-from adler.dataclasses.MPCORB import MPCORB
-from adler.dataclasses.SSObject import SSObject
-from adler.dataclasses.AdlerData import AdlerData
-from adler.dataclasses.dataclass_utilities import get_data_table
+from adler.objectdata.Observations import Observations
+from adler.objectdata.MPCORB import MPCORB
+from adler.objectdata.SSObject import SSObject
+from adler.objectdata.AdlerData import AdlerData
+from adler.objectdata.objectdata_utilities import get_data_table
 
 logger = logging.getLogger(__name__)
 

diff --git a/src/adler/dataclasses/MPCORB.py → src/adler/objectdata/MPCORB.py b/src/adler/dataclasses/MPCORB.py → src/adler/objectdata/MPCORB.py
@@ -1,6 +1,6 @@
 from dataclasses import dataclass
 
-from adler.dataclasses.dataclass_utilities import get_from_table, get_from_dictionary
+from adler.objectdata.objectdata_utilities import get_from_table, get_from_dictionary
 
 MPCORB_KEYS = {
     "mpcDesignation": str,

diff --git a/src/adler/dataclasses/Observations.py → src/adler/objectdata/Observations.py b/src/adler/dataclasses/Observations.py → src/adler/objectdata/Observations.py
@@ -1,7 +1,7 @@
 from dataclasses import dataclass, field
 import numpy as np
 
-from adler.dataclasses.dataclass_utilities import get_from_table, get_from_dictionary
+from adler.objectdata.objectdata_utilities import get_from_table, get_from_dictionary
 
 OBSERVATIONS_KEYS = {
     "diaSourceId": np.ndarray,

diff --git a/src/adler/dataclasses/SSObject.py → src/adler/objectdata/SSObject.py b/src/adler/dataclasses/SSObject.py → src/adler/objectdata/SSObject.py
@@ -1,7 +1,7 @@
 from dataclasses import dataclass, field
 import numpy as np
 
-from adler.dataclasses.dataclass_utilities import get_from_table, get_from_dictionary
+from adler.objectdata.objectdata_utilities import get_from_table, get_from_dictionary
 
 SSO_KEYS = {
     "discoverySubmissionDate": float,

diff --git a/src/adler/dataclasses/__init__.py → src/adler/objectdata/__init__.py b/src/adler/dataclasses/__init__.py → src/adler/objectdata/__init__.py
@@ -1,6 +1,6 @@
 from . import AdlerData
 from . import Observations
-from . import dataclass_utilities
+from . import objectdata_utilities
 from . import MPCORB
 from . import AdlerPlanetoid
 from . import SSObject
diff --git a/src/adler/dataclasses/dataclass_utilities.py → src/adler/objectdata/objectdata_utilities.py b/src/adler/dataclasses/dataclass_utilities.py → src/adler/objectdata/objectdata_utilities.py
diff --git a/tests/adler/dataclasses/test_AdlerData.py → tests/adler/objectdata/test_AdlerData.py b/tests/adler/dataclasses/test_AdlerData.py → tests/adler/objectdata/test_AdlerData.py
@@ -6,7 +6,7 @@
 
 from numpy.testing import assert_array_equal
 
-from adler.dataclasses.AdlerData import AdlerData
+from adler.objectdata.AdlerData import AdlerData
 from adler.utilities.tests_utilities import get_test_data_filepath
 
 # setting up the AdlerData object to be used for testing

diff --git a/.../adler/dataclasses/test_AdlerPlanetoid.py → ...s/adler/objectdata/test_AdlerPlanetoid.py b/.../adler/dataclasses/test_AdlerPlanetoid.py → ...s/adler/objectdata/test_AdlerPlanetoid.py
@@ -3,7 +3,7 @@
 from numpy.testing import assert_almost_equal
 
 from adler.utilities.tests_utilities import get_test_data_filepath
-from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid
+from adler.objectdata.AdlerPlanetoid import AdlerPlanetoid
 
 
 ssoid = 8268570668335894776

diff --git a/tests/adler/dataclasses/test_MPCORB.py → tests/adler/objectdata/test_MPCORB.py b/tests/adler/dataclasses/test_MPCORB.py → tests/adler/objectdata/test_MPCORB.py
@@ -1,8 +1,8 @@
 from numpy.testing import assert_almost_equal
 import numpy as np
 
-from adler.dataclasses.MPCORB import MPCORB
-from adler.dataclasses.dataclass_utilities import get_data_table
+from adler.objectdata.MPCORB import MPCORB
+from adler.objectdata.objectdata_utilities import get_data_table
 from adler.utilities.tests_utilities import get_test_data_filepath
 
 

diff --git a/tests/adler/dataclasses/test_Observations.py → tests/adler/objectdata/test_Observations.py b/tests/adler/dataclasses/test_Observations.py → tests/adler/objectdata/test_Observations.py
@@ -1,8 +1,8 @@
 from numpy.testing import assert_almost_equal
 import numpy as np
 
-from adler.dataclasses.Observations import Observations
-from adler.dataclasses.dataclass_utilities import get_data_table
+from adler.objectdata.Observations import Observations
+from adler.objectdata.objectdata_utilities import get_data_table
 from adler.utilities.tests_utilities import get_test_data_filepath