Issue 392 (#393)

* Fix tests on osx

* Changing the GHA to use the cache for PIP and Conda

* Disabling the full daijin_assemble run on the OSX tests as Portcullis is not (yet) available for it on Conda.

* Properly fix #392, with attending tests

* Fixed the log crash detected on OSX by @ljyanesm

Co-authored-by: ljyanesm <yanes.luis@gmail.com>

.github/workflows/python-package.yml

@@ -5,30 +5,46 @@ on:
   [ push, pull_request ]
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash -l {0}
     strategy:
       matrix:
         python-version: [ 3.8, 3.7, 3.6 ]
+        os: [ubuntu-latest, macos-latest]
     steps:
+    - name: Install system development tools
+      if: startsWith(runner.os, 'Linux')
+      run: |
+        export DEBIAN_FRONTEND=noninteractive
+        sudo apt update
+        sudo apt install -y build-essential zlib1g-dev zlib1g
     - uses: actions/checkout@v2
+    - uses: actions/cache@v2
+      if: startsWith(runner.os, 'Linux')
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+    - uses: actions/cache@v2
+      if: startsWith(runner.os, 'macOS')
+      with:
+        path: ~/Library/Caches/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
     - name: Cache conda
       id: cache-miniconda
-      uses: actions/cache@v1
+      uses: actions/cache@v2
       env:
         CACHE_NUMBER: 0
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         path: ~/conda_pkgs_dir
         key:
-          ${{ runner.os }}-conda-${{ hashFiles('./environment.yml') }}
-    - name: Install system development tools
-      run: |
-        export DEBIAN_FRONTEND=noninteractive
-        sudo apt update
-        sudo apt install -y build-essential zlib1g-dev zlib1g
+          ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('./environment.yml') }}
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: ${{ matrix.python-version }}
@@ -37,41 +53,59 @@ jobs:
         environment-file: ./environment.yml
         mamba-version: "*"
         use-mamba: true
-        channels: bioconda, conda-forge, defaults
-        use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-        auto-update-conda: true
-        activate-environment: "test"
-        auto-activate-base: false
+        channels: conda-forge, defaults
+        use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
+        # auto-update-conda: false
+        activate-environment: "mikado2"
+        # auto-activate-base: false
     - name: Install dependencies
       run: |
-        mamba install -y -c conda-forge -n test -- pytest-cov
         gcc --help
-        mamba install -n test -c bioconda -c conda-forge -y bioconda::portcullis stringtie scallop gmap star hisat2 prodigal blast diamond transdecoder conda-forge::gnuplot kallisto samtools gffread
         pip install -r requirements.txt
-        pip install Cython
+        pip install Cython pytest-cov
         python setup.py develop
     - name: Test light
       run: |
-        pytest -m slow Mikado/tests/test_system_calls.py::SerialiseChecker::test_subprocess_multi_empty_orfs
-    - name: Test full
+        pytest -m slow Mikado/tests/test_light.py::LightTest::test_subprocess_multi_empty_orfs
+    - name: Test full with coverage
+      if: startsWith(runner.os, 'Linux')
+      run: |
+        pytest --cov=Mikado --cov-report=xml --cov-config=.coveragerc -m 'not triage';
+    - name: Test full without coverage
+      if: startsWith(runner.os, 'macOS')
       run: |
-        pytest --cov=Mikado --cov-report=xml --cov-config=.coveragerc -m '(slow or not slow) and not triage';
+        pytest -m 'not triage';
     - name: Upload coverage to Codecov
+      if: startsWith(runner.os, 'Linux')
       uses: codecov/codecov-action@v1
     - name: Test daijin
+      if: startsWith(runner.os, 'Linux')
+      run: |
+        mamba install -c bioconda -c conda-forge -y bioconda::portcullis stringtie scallop gmap \
+          star hisat2 prodigal blast diamond transdecoder conda-forge::gnuplot kallisto samtools gffread;
+        cd sample_data; snakemake --latency-wait 60 --jobs 5 --cores 5
+    - name: Test daijin mikado
+      if: startsWith(runner.os, 'macOS')
       run: |
-        cd sample_data; snakemake --jobs 5 --cores 5
+        mamba install -c bioconda -c conda-forge -y prodigal blast diamond transdecoder kallisto samtools gffread;
+        cd sample_data; snakemake --latency-wait 60 --jobs 5 --cores 5 complete_no_assemble
     - name: Test fast
       run: |
         python -c "import Mikado; Mikado.test(label='fast')";
     - name: Test seed
       run: |
         # Check that the seed is set properly
-        mikado serialise --junctions sample_data/junctions.bed --genome Mikado/tests/chr5.fas.gz --transcripts Mikado/tests/check_seed.fa --configuration Mikado/tests/check_seed.yaml
-        mikado pick --log $(pwd)/pick.20a.log --procs 2 --seed 20 --fasta Mikado/tests/chr5.fas.gz  --json-conf Mikado/tests/check_seed.yaml -od 20a Mikado/tests/check_seed.gtf
-        mikado pick --log $(pwd)/pick.20b.log --procs 2 --seed 20 --fasta Mikado/tests/chr5.fas.gz  --json-conf Mikado/tests/check_seed.yaml -od 20b Mikado/tests/check_seed.gtf
-        mikado pick --log $(pwd)/pick.20c.log --procs 2 --seed 20 --fasta Mikado/tests/chr5.fas.gz  --json-conf Mikado/tests/check_seed.yaml -od 20c Mikado/tests/check_seed.gtf
-        mikado pick --log $(pwd)/pick.20d.log --procs 2 --seed 20 --fasta Mikado/tests/chr5.fas.gz  --json-conf Mikado/tests/check_seed.yaml -od 20d Mikado/tests/check_seed.gtf
-        mikado pick --log $(pwd)/pick.10.log --procs 2 --seed 1000 --fasta Mikado/tests/chr5.fas.gz  --json-conf Mikado/tests/check_seed.yaml -od 1000 Mikado/tests/check_seed.gtf
+        mikado serialise --junctions sample_data/junctions.bed --genome Mikado/tests/chr5.fas.gz \
+          --transcripts Mikado/tests/check_seed.fa --configuration Mikado/tests/check_seed.yaml;
+        mikado pick --log $(pwd)/pick.20a.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz  \
+          --configuration Mikado/tests/check_seed.yaml -od 20a Mikado/tests/check_seed.gtf;
+        mikado pick --log $(pwd)/pick.20b.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz  \
+          --configuration Mikado/tests/check_seed.yaml -od 20b Mikado/tests/check_seed.gtf;
+        mikado pick --log $(pwd)/pick.20c.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz  \
+          --json-conf Mikado/tests/check_seed.yaml -od 20c Mikado/tests/check_seed.gtf;
+        mikado pick --log $(pwd)/pick.20d.log --procs 2 --seed 20 --genome Mikado/tests/chr5.fas.gz  \
+          --json-conf Mikado/tests/check_seed.yaml -od 20d Mikado/tests/check_seed.gtf;
+        mikado pick --log $(pwd)/pick.10.log --procs 2 --seed 1000 --genome Mikado/tests/chr5.fas.gz  \
+          --json-conf Mikado/tests/check_seed.yaml -od 1000 Mikado/tests/check_seed.gtf;
         if [[ $(diff -q 20a 20b) || $(diff -q 20a 20c) || $(diff -q 20a 20d) ]]; then exit 1; fi
         if [[ ! $(diff -q 20a 1000) ]]; then exit 1; fi

CHANGELOG.md

@@ -1,3 +1,8 @@
+# Version 2.2.3
+
+Testing Mikado also on OSX, and adding OSX to the supported OSes in Conda.
+Fix [#392](https://github.com/EI-CoreBioinformatics/mikado/issues/392): 
+
 # Version 2.2.2
 
 Added the SHM capabilities to `mikado serialise` and `mikado compare`.