Improve conda

.github/workflows/conda_build.yml

@@ -4,8 +4,8 @@ on: [push, pull_request]
 
 jobs:
 
-  build:
-    name: ${{ matrix.python-version }} / ${{ matrix.os }}
+  analysis:
+    name: Analysis-Python ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -14,13 +14,71 @@ jobs:
         python-version: ['3.7']
     steps:
       - uses: actions/checkout@v2
+        with:
+          fetch-depth: '0'
       - uses: goanpeca/setup-miniconda@v1
+        with:
+          activate-environment: matchms-dev
+          environment-file: conda/environment-dev.yml
+          python-version: ${{ matrix.python-version }}
+      - name: Conda info
+        shell: bash -l {0}
+        run: conda info
+      - name: Python info
+        shell: bash -l {0}
+        run: |
+          which python
+          python --version
+      - name: Conda list
+        shell: bash -l {0}
+        run: conda list
+      - name: Check style against standards using prospector
+        shell: bash -l {0}
+        run: prospector -o grouped -o pylint:pylint-report.txt
+      - name: Check whether import statements are used consistently
+        shell: bash -l {0}
+        run: isort --check-only --diff --conda-env matchms-dev --recursive --wrap-length 79 --lines-after-imports 2 --force-single-line --no-lines-before FUTURE --no-lines-before STDLIB --no-lines-before THIRDPARTY --no-lines-before FIRSTPARTY --no-lines-before LOCALFOLDER matchms/ tests/ integration-tests/
+      - name: Build documentation
+        shell: bash -l {0}
+        run: |
+          make coverage html
+        working-directory: readthedocs/
+        env:
+          SPHINXOPTS: '-n'  # enable nit-picky mode
+      - name: Check documentation coverage threshold
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash -l {0}
+        run: |
+          cat readthedocs/_build/coverage/python.txt
+          UNCOVERED_MEMBERS=$(grep '*' readthedocs/_build/coverage/python.txt | wc -l)
+          UNCOVERED_MEMBERS_ALLOWED=25
+          if (( $UNCOVERED_MEMBERS > $UNCOVERED_MEMBERS_ALLOWED )) ; then echo "There are currently ${UNCOVERED_MEMBERS} uncovered members in the documentation, which is more than the ${UNCOVERED_MEMBERS_ALLOWED} allowed."; exit 1;fi
+          echo "The code is sufficiently documented with ${UNCOVERED_MEMBERS} uncovered members out of ${UNCOVERED_MEMBERS_ALLOWED} allowed.";
+      - name: Test
+        if: matrix.os != 'ubuntu-latest'
+        shell: bash -l {0}
+        run: |
+          python setup.py test
+      - name: Test with coverage
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash -l {0}
+        run: |
+          pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
+      - name: Correct coverage paths
+        if: matrix.os == 'ubuntu-latest'
+        run: sed -i "s+$PWD/++g" coverage.xml
+      - name: SonarCloud Scan
+        if: matrix.os == 'ubuntu-latest'
+        uses: sonarsource/sonarcloud-github-action@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+      - name: Create matchms-build environment
+        uses: goanpeca/setup-miniconda@v1
         with:
           activate-environment: matchms-build
-          auto-activate-base: false
-          auto-update-conda: true
           environment-file: conda/environment-build.yml
-          miniconda-version: 'latest'
           python-version: ${{ matrix.python-version }}
       - name: Show conda config
         shell: bash -l {0}
@@ -29,11 +87,15 @@ jobs:
           conda list
           conda config --show-sources
           conda config --show
+          conda env list
       - name: Python info
         shell: bash -l {0}
         run: |
           which python
           python --version
+      - name: Conda list
+        shell: bash -l {0}
+        run: conda list
       - name: Build the conda package
         shell: bash -l {0}
         run: |
@@ -44,3 +106,45 @@ jobs:
             --channel bioconda --channel conda-forge \
             --croot $BUILD_FOLDER \
             ./conda
+
+      - name: Create a test environment to test the package
+        uses: goanpeca/setup-miniconda@v1
+        with:
+          activate-environment: matchms-test
+          python-version: ${{ matrix.python-version }}
+      - name: Show conda config
+        shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
+          conda env list
+      - name: Python info
+        shell: bash -l {0}
+        run: |
+          which python
+          python --version
+      - name: Conda list
+        shell: bash -l {0}
+        run: conda list
+      - name: Test local conda package on unix
+        if: matrix.os != 'windows-latest'
+        shell: bash -l {0}
+        run: |
+          export BUILD_FOLDER=/tmp/matchms/_build
+          conda install \
+            --channel bioconda \
+            --channel conda-forge \
+            --channel file://${BUILD_FOLDER}/noarch/ \
+            matchms
+      - name: Test local conda package on windows
+        if: matrix.os == 'windows-latest'
+        shell: bash -l {0}
+        run: |
+          export BUILD_FOLDER=%TEMP%\matchms\_build
+          conda install \
+            --channel bioconda \
+            --channel conda-forge \
+            --channel file:\\${BUILD_FOLDER}\noarch\ \
+            matchms

.github/workflows/conda_publish.yml

@@ -7,22 +7,19 @@ on:
 jobs:
 
   publish:
-    name: ${{ matrix.python-version }} / ${{ matrix.os }}
+    name: Publish-Python ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        os: ['ubuntu-latest']
         python-version: ['3.7']
     steps:
       - uses: actions/checkout@v2
       - uses: goanpeca/setup-miniconda@v1
         with:
           activate-environment: matchms-build
-          auto-activate-base: false
-          auto-update-conda: true
           environment-file: conda/environment-build.yml
-          miniconda-version: 'latest'
           python-version: ${{ matrix.python-version }}
       - name: Show conda config
         shell: bash -l {0}
@@ -51,13 +48,25 @@ jobs:
         run: |
           export BUILD_FOLDER=/tmp/matchms/_build
           anaconda --token ${{ secrets.ANACONDA_TOKEN }} upload --user nlesc --force $BUILD_FOLDER/noarch/*.tar.bz2
+
+  testpublished:
+    name: Test Published-Python ${{ matrix.python-version }} / ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    needs: publish
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: ['3.7']
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: '0'
       - uses: goanpeca/setup-miniconda@v1
         with:
-          activate-environment: matchms-test
-          auto-activate-base: false
-          auto-update-conda: true
+          activate-environment: matchms-dev
+          environment-file: conda/environment-dev.yml
           channels: conda-forge,bioconda,nlesc
-          miniconda-version: 'latest'
           python-version: ${{ matrix.python-version }}
       - name: Show conda config
         shell: bash -l {0}
@@ -69,10 +78,7 @@ jobs:
       - name: Install the conda package from anaconda repository
         shell: bash -l {0}
         run: |
-          conda install conda build -c bioconda -c conda-forge -c nlesc matchms
-      - name: Install development dependencies
-        shell: bash -l {0}
-        run: python -m pip install -r conda/requirements-dev.txt
+          conda install -c bioconda -c conda-forge -c nlesc matchms
       - name: Test the installed conda package
         shell: bash -l {0}
         run: |

CHANGELOG.md

@@ -7,8 +7,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Unreleased
 
-- [diff](https://github.com/matchms/matchms/compare/0.3.1...HEAD) since 0.3.1 
-
 ### Added
 
 - ...
@@ -23,13 +21,38 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 
-- Moved ``spec2vec`` similarity related functionality from ``matchms`` to https://github.com/iomega/spec2vec   
+
+## [0.3.2] - 2020-05-20
+
+- [All changes](https://github.com/matchms/matchms/compare/0.3.1...HEAD) since 0.3.1
+
+### Changed
+
+- improve conda workflow [#244](https://github.com/matchms/matchms/pull/244)
+  - merge anaconda and python build workflows
+  - fix conda package install command in build workflow
+  - publish only on ubuntu machine
+- data folder is handled by setup.py but not meta.yml
+- split workflows into two parts
+- install conda package generated by the workflow
+- test conda packages on windows and unix separately
+- update workflow names
+- use default settings for conda action
+
+### Removed
+
+- remove python build badge [#244](https://github.com/matchms/matchms/pull/244)
+- Moved ``spec2vec`` similarity related functionality from ``matchms`` to [iomega/spec2vec](https://github.com/iomega/spec2vec)
+- removed build step in build workflow
+- removed conda build scripts: conda/build.sh and conda/bld.bat
+- removed conda/condarc.yml
+- removed conda_build_config.yaml
 
 ## [0.3.1] - 2020-05-19
 
 ### Added
 
-- improve conda package https://github.com/matchms/matchms/pull/225
+- improve conda package [#225](https://github.com/matchms/matchms/pull/225)
   - Build scripts for Windows and Unix(MacOS and Linux) systems
   - verify conda package after uploading to anaconda repository by installing it
   - conda package also includes `matchms/data` folder
@@ -47,9 +70,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - skip builds for Python 2.X
   - more flexible package versions
   - add deployment requirements to meta.yml
-- verify conda package https://github.com/matchms/matchms/pull/225
+- verify conda package [#225](https://github.com/matchms/matchms/pull/225)
   - use conda/environment.yml when building the package
-- split anaconda workflow https://github.com/matchms/matchms/pull/225
+- split anaconda workflow [#225](https://github.com/matchms/matchms/pull/225)
   - conda build: tests conda packages on every push and pull request
   - conda publish: publish and test conda package on release
   - update the developer instructions