Merge pull request #437 from alhom/master

Dev up-to-date to master, pruning the rtree

Author: alhom

.github/workflows/generate_reference_plots.yml

@@ -43,23 +43,19 @@ jobs:
             mkdir $DATAPATH
             touch $DATAPATH/.lockfile
             sbatch -W -o testpackage_gen_verf.txt --job-name gen_verf_plots ./testpackage/run_testpackage_generate_verf_set.sh $DATAPATH > jobid.txt
+            cat testpackage_gen_verf.txt
             export JOBID=$(grep -Po '\d+' jobid.txt)
             export SACCT_LOG=$(sacct -j $JOBID -o job,state,node | grep FAILED) 
             if [[ $SACCT_LOG ]]; then
               echo "Some job failed on a node"
               echo $SACCT_LOG 
               exit 1
             fi
-            cat testpackage_gen_verf.txt
-
-            python ./testpackage/testpackage_get_job_error.py testpackage_gen_verf.txt
+            .github/workflows/make_sbatch_job.sh run_testpackage_generate_verf_set $DATAPATH
             rm $DATAPATH/.lockfile
         - name: Comparing plotted data
           run: |
             export TMPDIR=$RUNNER_TEMP
             module load Python/3.10.4-GCCcore-11.3.0
             . CI_env/bin/activate
-            sbatch -W -o "testpackage_compare.txt" ./testpackage/run_compare.sh verf_set 
-            cat testpackage_compare.txt
-            python ./testpackage/testpackage_get_job_error.py testpackage_compare.txt
-     
+            .github/workflows/make_sbatch_job.sh run_compare verf_set 

.github/workflows/python-publish.yml

@@ -0,0 +1,74 @@
+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  workflow_dispatch: 
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+    strategy: 
+      matrix:
+        python-version: ["3.6","3,7","3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Build release distributions
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: testpypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      # url: https://pypi.org/p/YOURPROJECT
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          packages-dir: dist/

Documentation/README.rst

@@ -0,0 +1,16 @@
+==========================
+Building documentation
+==========================
+
+Documentation is automatically built and deployed using Sphinx as part of the continuous integration of the repository. If you want to build the documentation locally, you need to install a few more packages::
+
+   python -m venv CI_env
+   . CI_env/bin/activate
+   pip install ../analysator[all]
+   pip install sphinx numba yt geopack sphinx-rtd-theme
+
+after which you can generate e.g. the html documentation::
+
+   cd Documentation/sphinx
+   make dirhtml
+

Documentation/sphinx/analysator_exercises.rst

@@ -95,15 +95,15 @@ Setting the keword ``fsaved=True`` will add contours delienating all spatial cel
 Vector quantities can be overplotted as streamlines or vector maps. Give some a go!
 .. code-block:: python
 
-   :kword vectors:     Set to a vector variable to overplot (unit length vectors, color displays variable magnitude)
-   :kword vectordensity: Aim for how many vectors to show in plot window (default 100)
-   :kword vectorcolormap: Colormap to use for overplotted vectors (default: gray)
-   :kword vectorsize:  Scaling of vector sizes
+   :kwarg vectors:     Set to a vector variable to overplot (unit length vectors, color displays variable magnitude)
+   :kwarg vectordensity: Aim for how many vectors to show in plot window (default 100)
+   :kwarg vectorcolormap: Colormap to use for overplotted vectors (default: gray)
+   :kwarg vectorsize:  Scaling of vector sizes
 
-   :kword streamlines: Set to a vector variable to overplot as streamlines
-   :kword streamlinedensity: Set streamline density (default 1)
-   :kword streamlinecolor: Set streamline color (default white)
-   :kword streamlinethick: Set streamline thickness
+   :kwarg streamlines: Set to a vector variable to overplot as streamlines
+   :kwarg streamlinedensity: Set streamline density (default 1)
+   :kwarg streamlinecolor: Set streamline color (default white)
+   :kwarg streamlinethick: Set streamline thickness
 
 If a pre-generated fluxfunction file is available (only for 5D simulations), magnetic field lines can be plotted
 with greater accuracy than via streamlines. Flux functions are generated with the fluxfunction tool distributed as part of Vlasiator. A plotting example:
@@ -119,21 +119,21 @@ Several keywords exist for fine-tuning Analysator plot properties. As usual, the
 
 .. code-block:: python
 
-   :kword noborder:    Plot figure edge-to-edge without borders (default off)
-   :kword noxlabels:   Suppress x-axis labels and title
-   :kword noylabels:   Suppress y-axis labels and title
-   :kword scale:       Scale text size (default=1.0)
-   :kword thick:       line and axis thickness, default=1.0
-   :kword nocb:        Set to suppress drawing of colourbar
-   :kword internalcb:  Set to draw colorbar inside plot instead of outside. If set to a text
+   :kwarg noborder:    Plot figure edge-to-edge without borders (default off)
+   :kwarg noxlabels:   Suppress x-axis labels and title
+   :kwarg noylabels:   Suppress y-axis labels and title
+   :kwarg scale:       Scale text size (default=1.0)
+   :kwarg thick:       line and axis thickness, default=1.0
+   :kwarg nocb:        Set to suppress drawing of colourbar
+   :kwarg internalcb:  Set to draw colorbar inside plot instead of outside. If set to a text
                        string, tries to use that as the location, e.g. "NW","NE","SW","SW"
-   :kword highres:     Creates the image in high resolution, scaled up by this value (suitable for print).
-   :kword tickinterval: Interval at which to have ticks on axes (not colorbar)
-   :kword title:       string to use as plot title instead of time.
+   :kwarg highres:     Creates the image in high resolution, scaled up by this value (suitable for print).
+   :kwarg tickinterval: Interval at which to have ticks on axes (not colorbar)
+   :kwarg title:       string to use as plot title instead of time.
                        Special case: Set to "msec" to plot time with millisecond accuracy or "musec"
                        for microsecond accuracy. "sec" is integer second accuracy.
-   :kword cbtitle:     string to use as colorbar title instead of map name
-   :kword nooverwrite: Set to only perform actions if the target output file does not yet exist                  
+   :kwarg cbtitle:     string to use as colorbar title instead of map name
+   :kwarg nooverwrite: Set to only perform actions if the target output file does not yet exist                  
    
 Plotting 3D/6D simulation data
 ------------------------------

Documentation/sphinx/calculations.rst

@@ -4,3 +4,4 @@ calculations
 .. automodule:: analysator.calculations
    :members:
    :imported-members:
+   :ignore-module-all:

Documentation/sphinx/conf.py

@@ -22,7 +22,7 @@
 
 extensions = [
     'sphinx.ext.autodoc'
-    ]
+]
 
 templates_path = ['_templates']
 # Create a dummy _templates folder if it does not exist

Documentation/sphinx/index.rst

@@ -31,7 +31,7 @@ documentation for details.
    analysator_supported
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 2 
    :caption: Analysator reference
 
    plot
@@ -49,4 +49,4 @@ documentation for details.
    :maxdepth: 1
    :caption: About 
 
-   about
+   about

Documentation/sphinx/miscellaneous.rst

@@ -1,6 +1,7 @@
 miscellaneous
 ==================================
 
-.. automodule:: miscellaneous
+.. automodule:: analysator.miscellaneous
    :members:
    :imported-members:
+   :ignore-module-all:

Documentation/sphinx/plot.rst

@@ -1,8 +1,9 @@
+============================
 plot
 ============================
 
 .. automodule:: analysator.plot
    :members:
    :exclude-members: Version
    :imported-members:
-   
+   :ignore-module-all:   

Documentation/sphinx/vlsvfile.rst

@@ -1,8 +1,11 @@
 vlsvfile
 ============================
 
-VlsvFile is responsibe for implementing read and write functionality for the vlsv format, as well as defining data reducers and reduction pipelines. Some of this will be likely moved around to be more modular in some indefinite point in the future.
+VlsvFile is responsible for implementing read and write functionality for the vlsv format, as well as defining data reducers and reduction pipelines. Some of this will be likely moved around to be more modular in some indefinite point in the future.
 
 .. automodule:: analysator.vlsvfile
    :members:
    :imported-members:
+   :ignore-module-all:
+
+