Merge pull request #47 from antarcticrainforest/use-pip-for-install

Use pip for install

.github/workflows/tests.yml

@@ -17,59 +17,50 @@ jobs:
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Install micromamba environment
-        uses: mamba-org/provision-with-micromamba@main
-        with:
-          environment-name: test
-          environment-file: environment_ci.yml
-          extra-specs: |
-            python=3.10
-      - name: Lint with flake8 run1
-        run: |
-          flake8 src/tintx --count --select=E9,F63,F7,F82 --show-source --statistics
-      - name: Lint with flake8 run2
+      - name: Add conda to system path
         run: |
-          flake8 src/tintx --ignore E203 --count --exit-zero --max-complexity=15 --max-line-length=127 --statistics
-      - name: Black style check
+         # $CONDA is an environment variable pointing to the root of the miniconda directory
+          echo $CONDA/bin >> $GITHUB_PATH
+      - name: Creating conda environment for python 3.11
         run: |
-          black --check -t py310 -l 82 src/tintx
-      - name: Isort import check
+         conda create -n test -c conda-forge -y python=3.11 ffmpeg pip cartopy make
+      - name: Install dependencies
         run: |
-          isort --check --profile black -l 82 src/tintx
-      - name: mypy typechecks
+          conda run -n test python3 -m pip install -U -e .[tests]
+      - name: Linting the code
         run: |
-          mypy
-
+          conda run -n test make lint
   tests:
     name: tintX tests
     runs-on: ubuntu-latest
-    needs: [lint]
     defaults:
       run:
         shell: bash -l {0}
     strategy:
         max-parallel: 5
         matrix:
-          python-version: ["3.7", "3.8", "3.9", "3.10"]
+          python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
         fail-fast: false
     steps:
       - name: Checkout
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Install micromamba environment
-        uses: mamba-org/provision-with-micromamba@main
-        with:
-          environment-name: test
-          environment-file: environment_ci.yml
-          extra-specs: |
-            python=${{ matrix.python-version }}  
+      - name: Add conda to system path
+        run: |
+         # $CONDA is an environment variable pointing to the root of the miniconda directory
+          echo $CONDA/bin >> $GITHUB_PATH
+      - name: Creating conda environment for python ${{ matrix.python-version }}
+        run: |
+         conda create -n test -c conda-forge -y python=${{matrix.python-version}} ffmpeg pip cartopy make hdf5
+      - name: Install dependencies
+        run: |
+          conda run -n test python3 -m pip install -U -e .[tests,docs]
       - name: Test with pytest
         env:
-          MPLBACKEND: agg
           DATA_FILES: ./docs/source/_static/data
         run: |
-          python -m pytest -n auto --verbose --nbval-lax --cov-report xml:report.xml --cov=tintx --pyargs src/tintx
+          conda run -n test make test_coverage
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
         with:

Makefile

@@ -16,7 +16,7 @@ test:
 test_coverage:
 	python3 -m pytest -vv \
 	    --cov=$(PWD)/src/tintx --cov-report html:coverage_report \
-		--nbval-lax --current-env --cov-report=xml --junitxml report.xml
+		--nbval-lax --current-env --cov-report xml --junitxml report.xml
 	rm -rf '='
 	python3 -m coverage report
 
@@ -26,6 +26,8 @@ docs:
 
 
 lint:
-	mypy
-	black --check -t py310 -l 82 src
+	flake8 src/tintx --count --select=E9,F63,F7,F82 --show-source --statistics
 	flake8 src/tintx --ignore E203 --count --exit-zero --max-complexity=15 --max-line-length=127 --statistics
+	black --check -t py311 -l 82 src/tintx
+	isort --check --profile black -t py311 -l 82 src/tintx
+	mypy

README.md

@@ -5,7 +5,7 @@
 [![tests](https://github.com/antarcticrainforest/tintX/actions/workflows/tests.yml/badge.svg)](https://github.com/antarcticrainforest/tintX/actions)
 [![codecov](https://codecov.io/gh/antarcticrainforest/tintX/branch/main/graph/badge.svg)](https://codecov.io/gh/antarcticrainforest/tintX)
 [![PyPI version](https://badge.fury.io/py/tintx.svg)](https://badge.fury.io/py/tintx)
-[![Conda](https://anaconda.org/conda-forge/tintx/badges/installer/conda.svg)](https://anaconda.org/conda-forge/tintx)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/tintx/badges/version.svg)](https://anaconda.org/conda-forge/tintx)
 [![Latest](https://anaconda.org/conda-forge/tintx/badges/latest_release_date.svg)](https://anaconda.org/conda-forge/tintx)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/antarcticrainforest/tintX/main?labpath=Readme.ipynb)
 
@@ -14,11 +14,11 @@ Tint and tintX are easy-to-use storm cell tracking packages. While Tint is meant
 to be applied to radar data using the
 [py-ART toolkit](http://arm-doe.github.io/pyart/) tintX can
 be applied with any data - for example output from numerical weather prediction
-models. The original tracking algorithm that has been developed by a team of
+models. The original tracking algorithm has been developed by a team of
 researchers at Monash University [Raut et al. 2020](http://dx.doi.org/10.1175/JAMC-D-20-0119.1).
 
 ## Installation
-The `tintX` package can bin installed using the `conda-froge` conda channel:
+The `tintX` package can be installed using the `conda-froge` conda channel:
 
 ```console
 conda install -c conda-forge tintx
@@ -28,12 +28,11 @@ Alternatively the package can be installed with pip:
 ```console
 python -m pip install tintx
 ```
-if you don't have root access add the `--user` flag for a local installation.
 
 
 ## Usage
 Documentation can be found on the
-[official document page](https://tintx.readthedocs.io/en/latest/) of this
+[official documentation page](https://tintx.readthedocs.io/en/latest/) of this
 library.
 
 If you just want to try the usage and play with tracking data you can follow

docs/environment.yml

@@ -2,9 +2,10 @@ name: tintx
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.11
   - ipython
   - tintx
+  - hdf5
   - pip
   - pip:
       - sphinx-execute-code-python3

docs/source/I_Tracking_data_from_files.ipynb

@@ -3169,6 +3169,7 @@
     }
    ],
    "source": [
+    "# NBVAL_SKIP\n",
     "fig = plt.figure(figsize=(12,10))\n",
     "ax = fig.add_subplot(121, projection=crs.PlateCarree())\n",
     "\n",
@@ -4304,9 +4305,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "tintX kernel",
    "language": "python",
-   "name": "python3"
+   "name": "tintx"
   },
   "language_info": {
    "codemirror_mode": {
@@ -4318,7 +4319,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.5"
+   "version": "3.7.12"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

docs/source/index.rst

@@ -15,12 +15,12 @@ Welcome to tintX's documentation!
    :target: https://github.com/antarcticrainforest/tintX/actions
 .. image:: https://badge.fury.io/py/tintx.svg
     :target: https://badge.fury.io/py/tintx
-.. image:: https://anaconda.org/conda-forge/tintx/badges/installer/conda.svg
+.. image:: https://anaconda.org/conda-forge/tintx/badges/version.svg
     :target: https://anaconda.org/conda-forge/tintx
 .. image:: https://anaconda.org/conda-forge/tintx/badges/latest_release_date.svg
     :target: https://anaconda.org/conda-forge/tintx
 .. image:: https://mybinder.org/badge_logo.svg
- :target: https://mybinder.org/v2/gh/antarcticrainforest/tintX/main?labpath=Readme.ipynb
+    :target: https://mybinder.org/v2/gh/antarcticrainforest/tintX/main?labpath=Readme.ipynb
 
 TintX is an adaptation of the tint `tracking algorithm <https://github.com/openradar/TINT>`_.
 Tint and tintX are easy-to-use storm cell tracking packages.
@@ -34,7 +34,7 @@ How does the tint algorithm work?
 
 The original tracking algorithm that has been developed by a team of
 researchers at Monash University `Raut et al. 2020 <http://dx.doi.org/10.1175/JAMC-D-20-0119.1>`_.
-The tracking algorithm is designed to track storm cells using `phase
+The algorithm is designed to track storm cells using `phase
 correlation <https://en.wikipedia.org/wiki/Phase_correlation>`_
 between two consecutive time steps which is followed by an application of the
 `Hungarian Maximum Matching Algorithm
@@ -72,8 +72,6 @@ Alternatively the package can be installed with pip:
 
    python3 -m pip install tintx
 
-if you don't have root-access add the ``--user`` flag for a local installation.
-
 
 
 

pytest.ini

@@ -1,6 +1,5 @@
 [pytest]
 env =
-    PATH={PATH}:{PWD}/src/evaluation_system/tests/mocks/bin
-    EVALUATION_SYSTEM_CONFIG_FILE=compose/local-eval-system.conf
-    EVALUATION_SYSTEM_DRS_CONFIG_FILE=compose/drs_config.toml
     EVALUATION_SYSTEM_PLUGINS={PWD}/src/evaluation_system/tests/mocks,dummy
+    MPLBACKEND=agg
+    DATA_FILES={PWD}/docs/source/_static/data

setup.py

@@ -68,30 +68,32 @@ def find_version(*parts):
         "click",
         "cftime",
         "dask",
-        "pandas",
-        "tables",
+        "geopandas",
+        "matplotlib",
+        "netCDF4",
         "numpy",
+        "pandas",
+        "rasterio",
         "scipy",
-        "netCDF4",
-        "matplotlib",
-        "xarray",
+        "shapely",
+        "tables",
         "tqdm",
         "typing_extensions",
-        "rasterio",
-        "geopandas",
-        "shapely",
+        "xarray",
     ],
     extras_require={
         "tests": [
             "bash_kernel",
             "black",
+            "flake8",
+            "isort",
+            "mypy",
             "nbval",
             "pytest",
             "pytest-env",
             "pytest-cov",
+            "pytest-xdist",
             "testpath",
-            "flake8",
-            "mypy",
         ],
         "docs": [
             "bash_kernel",
@@ -100,9 +102,9 @@ def find_version(*parts):
             "ipywidgets",
             "h5netcdf",
             "mypy",
+            "nbsphinx",
             "pytest",
             "recommonmark",
-            "nbsphinx",
             "sphinx",
             "sphinxcontrib_github_alt",
             "sphinx-execute-code-python3",

src/tintx/__init__.py

@@ -16,4 +16,4 @@
 
 __all__ = ["RunDirectory"]
 
-__version__ = "2022.9.5"
+__version__ = "2022.12.2"

src/tintx/reader.py

@@ -10,8 +10,9 @@
 
 import geopandas as gpd
 import pandas as pd
+import pyproj
 import xarray as xr
-from cartopy.crs import CRS, AzimuthalEquidistant
+from cartopy.crs import AzimuthalEquidistant, Projection
 from cartopy.mpl.geoaxes import GeoAxesSubplot
 from matplotlib import pyplot as plt
 from shapely import wkt
@@ -77,7 +78,7 @@ def from_files(
         time_coord: str = "time",
         start: Optional[Union[str, datetime, pd.Timestamp]] = None,
         end: Optional[Union[str, datetime, pd.Timestamp]] = None,
-        crs: str = "epsg:3857",
+        crs: Union[str, pyproj.CRS, Projection] = "epsg:4326",
         **kwargs: Any,
     ) -> RunDirectory:
         """
@@ -106,10 +107,11 @@ def from_files(
             The name of the latitude vector/array, can be 1D or 2D
         time_coord: str, default: time
             The name of the time variable
-        crs: str (default: "epsg:3857")
-            wkt-string or epsg-string of Coordinate Reference System (CRS). If "aeqd",
-            CRS will be computed as AzimuthalEquidistant Projection from the geodetic
-            radar site coordinates "longitude" and "latitude".
+        crs: str, pyproj.Proj, cartopy.crs.Projection (default: "epsg:4326")
+            pyproj/cartopy projection object or string defining the Coordinate
+            Reference System (CRS). If "aeqd", CRS will be computed as
+            AzimuthalEquidistant Projection from the geodetic radar site
+            coordinates "longitude" and "latitude".
         kwargs:
             Additional keyword arguments that are passed to open the dataset
             with xarray
@@ -166,7 +168,7 @@ def __init__(
         time_coord: str = "time",
         x_coord: str = "lon",
         y_coord: str = "lat",
-        crs: str = "epsg:3857",
+        crs: Union[str, pyproj.CRS, Projection] = "epsg:4326",
         _files: Union[list[str], str] = "",
     ) -> None:
         if isinstance(dataset, xr.DataArray):
@@ -181,7 +183,16 @@ def __init__(
         self.start = convert_to_cftime(self.time.values[0])
         self.end = convert_to_cftime(self.time.values[-1])
         # transform crs to wkt in any case
-        self.crs = CRS(crs).to_wkt()
+        if isinstance(crs, Projection):
+            self.crs = pyproj.CRS(crs.proj4_init).to_wkt()
+        elif isinstance(crs, pyproj.CRS):
+            self.crs = crs.to_wkt()
+        elif isinstance(crs, str):
+            self.crs = pyproj.CRS(crs).to_wkt()
+        else:
+            raise TypeError(
+                "crs parameter must be a string or pyproj/cartopy " "projection"
+            )
         self._metadata_reader = MetaData(
             self.data,
             self.var_name,
@@ -276,7 +287,7 @@ def tracks(self) -> pd.DataFrame:
         # only convert into GeoDataFrame if geometry-column is available
         # for backwards compatibility reasons
         if "geometry" in self._tracks.columns:
-            return gpd.GeoDataFrame(self._tracks.copy(), crs=CRS(self.crs))
+            return gpd.GeoDataFrame(self._tracks.copy(), crs=pyproj.CRS(self.crs))
         else:
             return self._tracks