matchms · fdiblen · May 19, 2020 · May 19, 2020 · May 19, 2020 · May 19, 2020
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
@@ -14,26 +14,92 @@ jobs:
         python-version: ['3.7']
     steps:
       - uses: actions/checkout@v2
+        with:
+          fetch-depth: '0'
       - uses: goanpeca/setup-miniconda@v1
+        with:
+          auto-update-conda: false
+          python-version: ${{ matrix.python-version }}
+          activate-environment: matchms-dev
+          environment-file: conda/environment-dev.yml
+          condarc-file: conda/condarc.yml
+          auto-activate-base: true
+      - name: Conda info
+        shell: bash -l {0}
+        run: conda info
+      - name: Python info
+        shell: bash -l {0}
+        run: |
+          which python
+          python --version
+      - name: Conda list
+        shell: bash -l {0}
+        run: conda list
+      - name: Check style against standards using prospector
+        shell: bash -l {0}
+        run: prospector -o grouped -o pylint:pylint-report.txt
+      - name: Check whether import statements are used consistently
+        shell: bash -l {0}
+        run: isort --check-only --diff --conda-env matchms-dev --recursive --wrap-length 79 --lines-after-imports 2 --force-single-line --no-lines-before FUTURE --no-lines-before STDLIB --no-lines-before THIRDPARTY --no-lines-before FIRSTPARTY --no-lines-before LOCALFOLDER matchms/ tests/ integration-tests/
+      - name: Build
+        shell: bash -l {0}
+        run: |
+          python setup.py build
+      - name: Build documentation
+        shell: bash -l {0}
+        run: |
+          make coverage html
+        working-directory: readthedocs/
+        env:
+          SPHINXOPTS: '-n'  # enable nit-picky mode
+      - name: Check documentation coverage threshold
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash -l {0}
+        run: |
+          cat readthedocs/_build/coverage/python.txt
+          UNCOVERED_MEMBERS=$(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
+          auto-activate-base: true
+          auto-update-conda: false
           environment-file: conda/environment-build.yml
           miniconda-version: 'latest'
           python-version: ${{ matrix.python-version }}
-      - name: Show conda config
+      - name: Conda info
         shell: bash -l {0}
-        run: |
-          conda info
-          conda list
-          conda config --show-sources
-          conda config --show
+        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: Build the conda package
         shell: bash -l {0}
         run: |
@@ -44,3 +110,12 @@ jobs:
             --channel bioconda --channel conda-forge \
             --croot $BUILD_FOLDER \
             ./conda
+      - name: Test local conda package
+        shell: bash -l {0}
+        run: |
+          export BUILD_FOLDER=/tmp/matchms/_build
+          conda install \
+            --channel bioconda \
+            --channel conda-forge \
+            --channel file://${BUILD_FOLDER}/noarch/ \
+            matchms
diff --git a/.github/workflows/conda_publish.yml b/.github/workflows/conda_publish.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        os: ['ubuntu-latest']
         python-version: ['3.7']
     steps:
       - uses: actions/checkout@v2
@@ -69,7 +69,7 @@ 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
+          conda install -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

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,11 +7,24 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.3.2] - 2020-05-20
+
+### 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
+
+### Removed
+
+- remove python build badge [#244](https://github.com/matchms/matchms/pull/244)
+
 ## [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
@@ -29,9 +42,9 @@ 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

diff --git a/README.rst b/README.rst
@@ -28,7 +28,7 @@ Vector representation and similarity measure for mass spectrometry data.
    * - **Other best practices**
      -
    * - Continuous integration
-     - |Python Build| |Anaconda Build| |Anaconda Publish|
+     - |Anaconda Build| |Anaconda Publish|
    * - Documentation
      - |ReadTheDocs Badge|
    * - Code Quality
@@ -75,10 +75,6 @@ Vector representation and similarity measure for mass spectrometry data.
    :target: https://sonarcloud.io/component_measures?id=matchms_matchms&metric=Coverage&view=list
    :alt: Sonarcloud Coverage
 
-.. |Python Build| image:: https://github.com/matchms/matchms/workflows/Python%20Build/badge.svg
-   :target: https://github.com/matchms/matchms/actions?query=workflow%3A%22Python%20Build%22
-   :alt: Python Build
-
 .. |Anaconda Build| image:: https://github.com/matchms/matchms/workflows/Anaconda%20Build/badge.svg
    :target: https://github.com/matchms/matchms/actions?query=workflow%3A%22Anaconda%20Build%22
    :alt: Anaconda Build
@@ -191,7 +187,7 @@ installation of this conda package works with:
   conda install \
     --channel bioconda \
     --channel conda-forge \
-    --channel file://${CONDA_PREFIX}/output/noarch/ \
+    --channel file://${CONDA_PREFIX}/noarch/ \
     matchms
 
 To publish the package on anaconda cloud, do:

diff --git a/conda/build.sh b/conda/build.sh
@@ -5,6 +5,6 @@ env
 
 $PYTHON -m pip install --no-deps --ignore-installed . -vv
 
-# Copy data folder
-mkdir -p $PREFIX/site-packages/matchms/data
-cp matchms/data/* $PREFIX/site-packages/matchms/data/
+# # Copy data folder
+# mkdir -p $PREFIX/site-packages/matchms/data
+# cp matchms/data/* $PREFIX/site-packages/matchms/data/
diff --git a/conda/conda_build_config.yaml b/conda/conda_build_config.yaml
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "matchms" %}
-{% set version = "0.3.1" %}
+{% set version = "0.3.2" %}
 
 package:
   name: {{ name|lower }}

diff --git a/matchms/__version__.py b/matchms/__version__.py
@@ -1 +1 @@
-__version__ = '0.3.1'
+__version__ = '0.3.2'
diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.1
+current_version = 0.3.2
 
 [bumpversion:file:conda/meta.yaml]
 search = set version = "{current_version}"
@@ -13,8 +13,7 @@ replace = __version__ = '{new_version}'
 description-file = README.rst
 
 [aliases]
-# Define `python setup.py test`
-test=pytest
+test = pytest
 
 [coverage:run]
 branch = True
@@ -25,7 +24,6 @@ testpaths = tests integration-tests
 python_classes = *TestSuite
 junit_family = xunit2
 
-# Define `python setup.py build_sphinx`
 [build_sphinx]
 source-dir = docs
 build-dir = docs/_build

diff --git a/setup.py b/setup.py
@@ -55,5 +55,6 @@
     ],
     extras_require={
         # see conda/environment.yml
-    }
+    },
+    package_data={'matchms': ['data/*.yaml']},
 )