Merge pull request #109 from antarcticrainforest/use-tox

Use tox

.coveragerc

@@ -1,7 +1,39 @@
+# .coveragerc to control coverage.py
 [run]
-omit = */test/*
+branch = False
+omit = .converage*
+       */tests/*
+       */__main__.py
 concurrency = multiprocessing
-
 [report]
+fail_under = 97
+# Regexes for lines to exclude from consideration
 exclude_lines =
+    # Have to re-enable the standard pragma
     pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+    def _post_url(self)
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+    except KeyboardInterrupt:
+    except ImportError:
+    except RuntimeError
+    raise SystemExit
+
+    # Don't complain about the Completer class
+    class Completer
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if perf_file *:
+    p_col = *
+    f_col = *
+    q_col = *
+    if __name__ == .__main__.:
+
+ignore_errors = False

.github/workflows/tests.yml

@@ -28,15 +28,18 @@ jobs:
         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 3.11
+      - name: Creating conda environment
         run: |
-         conda create -n test -c conda-forge -y python=3.11 pip cartopy make
-      - name: Install dependencies
+         conda create -n test -c conda-forge -y ipykernel bash_kernel ffmpeg cartopy make pandoc tox
+      - name: Setup jupyter kernel
         run: |
-          conda run -n test python3 -m pip install -U -e .[tests]
+          conda run -n test python3 -m ipykernel install --name tintx --display-name "tintX kernel" --env DATA_FILES ${PWD}/docs/source/_static/data --user
+          conda run -n test python3 -m bash_kernel.install
       - name: Linting the code
+        env:
+          DATA_FILES: ./docs/source/_static/data
         run: |
-          conda run -n test make lint
+          conda run -n test tox --parallel-no-spinner -p -e lint,docs
   tests:
     name: tintX tests
     runs-on: ubuntu-latest
@@ -46,7 +49,7 @@ jobs:
     strategy:
         max-parallel: 5
         matrix:
-          python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+          python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         fail-fast: false
     steps:
       - name: Checkout
@@ -59,10 +62,7 @@ jobs:
           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]
+         conda create -n test -c conda-forge -y python=${{matrix.python-version}} ipykernel bash_kernel ffmpeg cartopy make pandoc tox
       - name: Setup jupyter kernel
         run: |
           conda run -n test python3 -m ipykernel install --name tintx --display-name "tintX kernel" --env DATA_FILES ${PWD}/docs/source/_static/data --user
@@ -71,11 +71,12 @@ jobs:
         env:
           DATA_FILES: ./docs/source/_static/data
         run: |
-          conda run -n test make all
+          conda run -n test tox -e tests
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
         with:
-          file: ./report.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
   dependabot:
     name: Merge PR by dependabot
     runs-on: ubuntu-latest

.gitignore

@@ -4,6 +4,7 @@ build/*
 coverage_report.xml
 *.egg-info
 *.ipynb_checkpoints/*
+.tox/*
 docs/source/.ipynb_checkpoints/
 docs/source/_build/
 report.xml

MANIFEST.in

@@ -1,4 +1,2 @@
 include LICENSE
 include README.md
-include .coveragerc
-include pytest.ini

Makefile

@@ -10,7 +10,7 @@ install:
 	python3 -m bash_kernel.install
 
 test:
-	python3 -m pytest -vv $(PWD)/src/tintx/test
+	python3 -m pytest -vv $(PWD)/tests
 	rm -rf '='
 
 test_notebooks:

README.md

@@ -48,12 +48,11 @@ possible to tintX:
 
 - [ ] Create a fork of [this repository](https://github.com/antarcticrainforest/tintX)
      and clone this fork (not the original code)
+- [ ] Install the code in development mode: `python3 -m pip install -e .[dev]`
 - [ ] Create a new branch in the forked repository `git checkout -b my-new-branch`
 - [ ] Add your changes
 - [ ] Make sure all tests are sill running. To do so run the following commands
-    - make lint
-    - make test
-    - make docs
+    - tox
 - [ ] Create a new pull request to the `main` branch of the
      [original repository](https://github.com/antarcticrainforest/tintX).
 ### Adding new Jupyter examples

docs/environment.yml

@@ -2,11 +2,12 @@ name: tintx
 channels:
   - conda-forge
 dependencies:
-  - python=3.11
+  - python=3.12
   - ipython
   - tintx
   - geopandas
   - hdf5
+  - pandoc
   - pip
   - pip:
       - furo

docs/source/III_Using_the_command_line_interface.ipynb

@@ -176,7 +176,7 @@
       "\n",
       "  Arguments:\n",
       "\n",
-      "  input_files:     Filename of the HDF5 file contaning the tracking data.\n",
+      "  input_files:     Filename of the HDF5 file containing the tracking data.\n",
       "\n",
       "Options:\n",
       "  -o, --output FILE        Path to a visualisation of the tracking. If `None`\n",

docs/source/II_Tracking_already_loaded_datasets.ipynb

@@ -997,7 +997,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can now simply create a `RunDicrectory` object by directly initialising the class. Since the `time`, `lon` and `lat` dimensions already have the default names we don't have to pass the `x_coord`, `y_coord` or `time_coord` keywords:"
+    "We can now simply create a `RunDirectory` object by directly initialising the class. Since the `time`, `lon` and `lat` dimensions already have the default names we don't have to pass the `x_coord`, `y_coord` or `time_coord` keywords:"
    ]
   },
   {