fix github action by updating pytest from conda to mamba (#129)

* first attempt * fixed indentation * fixed indentation * updated pyincore version in environment.yml * added in-core channel in environmet.yml * updated readme * updated mamba for conda build * updated mamba command * used mambabuild * install boa * added mamba shell * added micromamba on conda build * rollback to previous conda build * upgraded pyincore version * updated pyincore to 1.11.0 * revert all back * make conda build to use python 3.9 * added mamba shell * added args * fixed version information * updated changelog
IN-CORE · Aug 11, 2023 · cef0ad3 · cef0ad3
1 parent 295dd5a
commit cef0ad3
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Showing 9 changed files with 142 additions and 120 deletions.
diff --git a/.github/workflows/conda.yaml b/.github/workflows/conda.yaml
@@ -26,7 +26,7 @@ jobs:
           if [ "${{ github.event.release.tag_name }}" != "" ]; then
             version=$(echo ${{ github.event.release.tag_name }} | sed 's/^v//')
           else
-            version="$(awk -F= '/^PACKAGE_VERSION/ { print $2}' pyincore-viz/globals.py | sed 's/[ "]//g').${{ github.run_number }}"
+            version="$(awk -F= '/^PACKAGE_VERSION/ { print $2}' pyincore_viz/globals.py | sed 's/[ "]//g').${{ github.run_number }}"
           fi
           echo "VERSION=${version}" >> $GITHUB_ENV
           echo "VERSION=${version}"
@@ -49,23 +49,28 @@ jobs:
           key:
             ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
 
-      - name: Install miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Install micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          miniconda-version: "latest"
-          python-version: 3.8
-          use-mamba: true
-          mamba-version: "*"
-          channels: conda-forge,in-core
-          use-only-tar-bz2: true
-          conda-build-version: "*"
+          create-args: >-
+            python=3.9
+            conda
+          environment-file: environment.yml
+          generate-run-shell: true
+          condarc: |
+            channels:
+              - IN-CORE
+              - conda-forge
+              - defaults
 
       - name: Build conda package
         run: |
+          conda install conda-build
           mkdir dist
           conda build --output-folder dist \
                       --label ${{ env.LABEL }} \
                       recipes
+        shell: micromamba-shell {0}
 
       - name: Upload conda package
         if: github.event_name == 'release'
@@ -75,6 +80,7 @@ jobs:
                           --user IN-CORE \
                           --label ${{ env.LABEL }} \
                           dist/*/pyincore-viz-${{ env.VERSION }}-*.tar.bz2
+        shell: micromamba-shell {0}
 
       - name: Upload binaries to release
         if: github.event_name == 'release'

diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
@@ -13,6 +13,11 @@ jobs:
   # ----------------------------------------------------------------------
   unit-test:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        vars: [ { python-version: '3.8', sleep: '0s' }, { python-version: '3.9', sleep: '60s' } ]
+#                { python-version: '3.10', sleep: '120s' }, { python-version: '3.11', sleep: '180s' } ]
+    name: Python ${{ matrix.vars.python-version }} Test
     steps:
       - name: Checkout source code
         uses: actions/checkout@v2
@@ -28,25 +33,28 @@ jobs:
             ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
             hashFiles('environment.yml') }}
 
-      - name: Install miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Install micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
-          miniconda-version: "latest"
-          mamba-version: "*"
-          use-mamba: true
-          python-version: 3.8
-          activate-environment: base
-          channels: conda-forge,in-core
+          create-args: >-
+            python=${{ matrix.vars.python-version }}
+            pytest
           environment-file: environment.yml
-          use-only-tar-bz2: true
-          conda-build-version: "*"
+          generate-run-shell: true
+
+      - name: Sleep for ${{ matrix.vars.sleep }} to avoid multiple pytests run concurrently
+        uses: jakejarvis/wait-action@master
+        with:
+          time: ${{ matrix.vars.sleep }}
 
       - name: Run pyincore viz tests with pytest
         run: |
           echo "${{secrets.PYTEST_USER_TOKEN}}" > tests/pyincore_viz/.incorepw
-          $CONDA/bin/pytest --cache-clear -s tests/pyincore_viz/test_pyincore_viz.py --junitxml=test-reports/viz_results.xml
+          python -m pytest tests/pyincore_viz/test_pyincore_viz.py
+        shell: micromamba-shell {0}
 
       - name: Run analysis viz tests with pytest
         run: |
           echo "${{secrets.PYTEST_USER_TOKEN}}" > tests/pyincore_viz/.incorepw
-          $CONDA/bin/pytest --cache-clear -s tests/pyincore_viz/test_analysis_viz.py --junitxml=test-reports/analysis_results.xml
+          python -m pytest tests/pyincore_viz/test_analysis_viz.py
+        shell: micromamba-shell {0}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
+## [Unreleased]
+### Changed
+- Pytest changed to use micromamba [#128](https://github.com/IN-CORE/pyincore-viz/issues/128)
+
+### Fixed
+- Conda package building and uploading github action [#131](https://github.com/IN-CORE/pyincore-viz/issues/131)
+
 ## [1.8.2] - 2023-06-14
 
 ### Changed

diff --git a/environment.yml b/environment.yml
@@ -2,6 +2,7 @@ name: pyincore_viz
 channels:
   - conda-forge
   - defaults
+  - in-core
 dependencies:
   - gdal
   - branca>=0.3.0
@@ -18,7 +19,7 @@ dependencies:
   - pandas>=0.24.1
   - pillow
   - pycodestyle>=2.6.0
-  - pyincore>=1.7.0
+  - pyincore>=1.11.0
   - pytest>=3.9.0
   - python-jose>=3.0
   - rasterio>=1.3.3
diff --git a/recipes/meta.yaml b/recipes/meta.yaml
@@ -47,7 +47,7 @@ requirements:
     - owslib>=0.17.1
     - pandas>=0.24.1
     - pillow
-    - pyincore>=1.7.0
+    - pyincore>=1.11.0
     - rasterio>=1.3.3
 
 test:

diff --git a/requirements.min b/requirements.min
@@ -13,7 +13,7 @@ owslib>=0.17.1
 pandas>=0.24.1
 pillow
 pycodestyle>=2.6.0
-pyincore>=1.7.0
+pyincore>=1.11.0
 pytest>=3.9.0
 python-jose>=3.0
 rasterio>=1.3.3
diff --git a/requirements.txt b/requirements.txt
@@ -13,7 +13,7 @@ owslib>=0.17.1
 pandas>=0.24.1
 pillow
 pycodestyle>=2.6.0
-pyincore>=1.7.0
+pyincore>=1.11.0
 pytest>=3.9.0
 python-jose>=3.0
 rasterio>=1.3.3
diff --git a/setup.py b/setup.py
@@ -66,7 +66,7 @@
         'owslib>=0.17.1',
         'pandas>=0.24.1',
         'pillow',
-        'pyincore>=1.7.0',
+        'pyincore>=1.11.0',
         'rasterio>=1.3.3'
     ],
 

diff --git a/versions.md b/versions.md
@@ -4,96 +4,96 @@ This file is autogenerated and lists the latest versions of all dependencies. Th
 
 | PIP Package | Conda Package | Required Version | Matched Version (pip) |
 |-------------|---------------|------------------|-----------------------|
-| branca | | \>=0.3.0| 0.6.0 |
-| contextily | | \>=1.0.0| 1.3.0 |
-| deprecated | | | 1.2.14 |
-| geopandas | | \>=0.6.1| 0.13.2 |
-| ipyleaflet | | \>=0.16.0| 0.17.3 |
-| ipywidgets | | \>=7.6.0| 8.0.7 |
-| lxml | | \>=4.6.3| 4.9.3 |
-| matplotlib | | \>=2.1.0| 3.7.2 |
-| networkx | | \>=2.2| 3.1 |
-| numpy | | \>=1.16.1| 1.25.2 |
-| owslib | | \>=0.17.1| 0.29.2 |
-| pandas | | \>=0.24.1| 2.0.3 |
-| pillow | | | 10.0.0 |
-| pycodestyle | | \>=2.6.0| 2.11.0 |
-| pyincore | | \>=1.7.0| 1.12.0a1 |
-| pytest | | \>=3.9.0| 7.4.0 |
-| python-jose | | \>=3.0| 3.3.0 |
-| rasterio | | \>=1.3.3| 1.3.8 |
-| affine | | | 2.4.0 |
-| asttokens | | | 2.2.1 |
-| attrs | | | 23.1.1.dev47 |
-| backcall | | | 0.2.0 |
-| certifi | | | 2023.7.22 |
-| charset-normalizer | | | 3.2.0 |
-| click | | | 8.1.6 |
-| click-plugins | | | 1.1.1 |
-| cligj | | | 0.7.2 |
-| comm | | | 0.1.3 |
-| contourpy | | | 1.1.0 |
-| cycler | | | 0.11.0 |
-| debugpy | | | 1.6.7 |
-| decorator | | | 5.1.1 |
-| ecdsa | | | 0.18.0 |
-| exceptiongroup | | | 1.1.2 |
-| executing | | | 1.2.0 |
-| fiona | | | 1.9.4.post1 |
-| fonttools | | | 4.41.1 |
-| geographiclib | | | 2.0 |
-| geopy | | | 2.3.0 |
-| idna | | | 3.4 |
-| iniconfig | | | 2.0.0 |
-| ipykernel | | | 6.25.0 |
-| ipython | | | 8.14.0 |
-| jedi | | | 0.19.0 |
-| jinja2 | | | 3.1.2 |
-| joblib | | | 1.3.1 |
-| jupyter-client | jupyter_client | | 8.3.0 |
-| jupyter-core | jupyter_core | | 5.3.1 |
-| jupyterlab-widgets | jupyterlab_widgets | | 3.0.8 |
-| kiwisolver | | | 1.4.4 |
-| markupsafe | | | 2.1.3 |
-| matplotlib-inline | | | 0.1.6 |
-| mercantile | | | 1.2.1 |
-| nest-asyncio | | | 1.5.7 |
-| packaging | | | 23.1 |
-| parso | | | 0.8.3 |
-| pexpect | | | 4.8.0 |
-| pickleshare | | | 0.7.5 |
-| platformdirs | | | 3.10.0 |
-| pluggy | | | 1.2.0 |
-| ply | | | 3.11 |
-| prompt-toolkit | | | 3.0.39 |
-| psutil | | | 5.9.5 |
-| ptyprocess | | | 0.7.0 |
-| pure-eval | | | 0.2.2 |
-| pyasn1 | | | 0.5.0 |
-| pygments | | | 2.15.1 |
-| pyomo | | | 6.6.1 |
-| pyparsing | | | 3.0.9 |
-| pyproj | | | 3.6.0 |
-| python-dateutil | | | 2.8.2 |
-| pytz | | | 2023.3 |
-| pyyaml | | | 6.0.1 |
-| pyzmq | | | 25.1.1b2 |
-| requests | | | 2.31.0 |
-| rsa | | | 4.9 |
-| rtree | | | 1.0.1 |
-| scipy | | | 1.11.1 |
-| shapely | | | 2.0.1 |
-| six | | | 1.16.0 |
-| snuggs | | | 1.4.7 |
-| stack-data | stack_data | | 0.6.2 |
-| tomli | | | 2.0.1 |
-| tornado | | | 6.4.dev1 |
-| traitlets | | | 5.9.0 |
-| traittypes | | | 0.2.1 |
-| tzdata | | | 2023.3 |
-| urllib3 | | | 2.0.4 |
-| wcwidth | | | 0.2.6 |
-| widgetsnbextension | | | 4.0.8 |
-| wntr | | | 1.0.0 |
-| wrapt | | | 1.15.0 |
-| xyzservices | | | 2023.7.0 |
+| branca | | \>=0.3.0         | 0.6.0 |
+| contextily | | \>=1.0.0         | 1.3.0 |
+| deprecated | |                  | 1.2.14 |
+| geopandas | | \>=0.6.1         | 0.13.2 |
+| ipyleaflet | | \>=0.16.0        | 0.17.3 |
+| ipywidgets | | \>=7.6.0         | 8.0.7 |
+| lxml | | \>=4.6.3         | 4.9.3 |
+| matplotlib | | \>=2.1.0         | 3.7.2 |
+| networkx | | \>=2.2           | 3.1 |
+| numpy | | \>=1.16.1        | 1.25.2 |
+| owslib | | \>=0.17.1        | 0.29.2 |
+| pandas | | \>=0.24.1        | 2.0.3 |
+| pillow | |                  | 10.0.0 |
+| pycodestyle | | \>=2.6.0         | 2.11.0 |
+| pyincore | | \>=1.11.0        | 1.12.0a1 |
+| pytest | | \>=3.9.0         | 7.4.0 |
+| python-jose | | \>=3.0           | 3.3.0 |
+| rasterio | | \>=1.3.3         | 1.3.8 |
+| affine | |                  | 2.4.0 |
+| asttokens | |                  | 2.2.1 |
+| attrs | |                  | 23.1.1.dev47 |
+| backcall | |                  | 0.2.0 |
+| certifi | |                  | 2023.7.22 |
+| charset-normalizer | |                  | 3.2.0 |
+| click | |                  | 8.1.6 |
+| click-plugins | |                  | 1.1.1 |
+| cligj | |                  | 0.7.2 |
+| comm | |                  | 0.1.3 |
+| contourpy | |                  | 1.1.0 |
+| cycler | |                  | 0.11.0 |
+| debugpy | |                  | 1.6.7 |
+| decorator | |                  | 5.1.1 |
+| ecdsa | |                  | 0.18.0 |
+| exceptiongroup | |                  | 1.1.2 |
+| executing | |                  | 1.2.0 |
+| fiona | |                  | 1.9.4.post1 |
+| fonttools | |                  | 4.41.1 |
+| geographiclib | |                  | 2.0 |
+| geopy | |                  | 2.3.0 |
+| idna | |                  | 3.4 |
+| iniconfig | |                  | 2.0.0 |
+| ipykernel | |                  | 6.25.0 |
+| ipython | |                  | 8.14.0 |
+| jedi | |                  | 0.19.0 |
+| jinja2 | |                  | 3.1.2 |
+| joblib | |                  | 1.3.1 |
+| jupyter-client | jupyter_client |                  | 8.3.0 |
+| jupyter-core | jupyter_core |                  | 5.3.1 |
+| jupyterlab-widgets | jupyterlab_widgets |                  | 3.0.8 |
+| kiwisolver | |                  | 1.4.4 |
+| markupsafe | |                  | 2.1.3 |
+| matplotlib-inline | |                  | 0.1.6 |
+| mercantile | |                  | 1.2.1 |
+| nest-asyncio | |                  | 1.5.7 |
+| packaging | |                  | 23.1 |
+| parso | |                  | 0.8.3 |
+| pexpect | |                  | 4.8.0 |
+| pickleshare | |                  | 0.7.5 |
+| platformdirs | |                  | 3.10.0 |
+| pluggy | |                  | 1.2.0 |
+| ply | |                  | 3.11 |
+| prompt-toolkit | |                  | 3.0.39 |
+| psutil | |                  | 5.9.5 |
+| ptyprocess | |                  | 0.7.0 |
+| pure-eval | |                  | 0.2.2 |
+| pyasn1 | |                  | 0.5.0 |
+| pygments | |                  | 2.15.1 |
+| pyomo | |                  | 6.6.1 |
+| pyparsing | |                  | 3.0.9 |
+| pyproj | |                  | 3.6.0 |
+| python-dateutil | |                  | 2.8.2 |
+| pytz | |                  | 2023.3 |
+| pyyaml | |                  | 6.0.1 |
+| pyzmq | |                  | 25.1.1b2 |
+| requests | |                  | 2.31.0 |
+| rsa | |                  | 4.9 |
+| rtree | |                  | 1.0.1 |
+| scipy | |                  | 1.11.1 |
+| shapely | |                  | 2.0.1 |
+| six | |                  | 1.16.0 |
+| snuggs | |                  | 1.4.7 |
+| stack-data | stack_data |                  | 0.6.2 |
+| tomli | |                  | 2.0.1 |
+| tornado | |                  | 6.4.dev1 |
+| traitlets | |                  | 5.9.0 |
+| traittypes | |                  | 0.2.1 |
+| tzdata | |                  | 2023.3 |
+| urllib3 | |                  | 2.0.4 |
+| wcwidth | |                  | 0.2.6 |
+| widgetsnbextension | |                  | 4.0.8 |
+| wntr | |                  | 1.0.0 |
+| wrapt | |                  | 1.15.0 |
+| xyzservices | |                  | 2023.7.0 |