Merge pull request #372 from deeptools/changeOSXAzure

Change osx azure
deeptools · Jan 14, 2022 · a88048f · a88048f
2 parents 1327d35 + d5a7c46
commit a88048f
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Showing 4 changed files with 34 additions and 24 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -58,7 +58,7 @@ before_install:
 - conda update -q conda
 - conda info -a
 install:
-- conda install --yes -c bioconda -c conda-forge python=$TRAVIS_PYTHON_VERSION --file requirements_travis.txt
+- conda install --yes -c bioconda -c conda-forge python=$TRAVIS_PYTHON_VERSION --file requirements_CI.txt
 - conda install --yes -c conda-forge -c bioconda pytest nose ghostscript pathlib
 - python setup.py install
 script:

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -15,6 +15,8 @@ jobs:
         python.version: '3.7'
       Python38:
         python.version: '3.8'
+      Python39:
+        python.version: '3.9'
 
   steps:
   - bash: |
@@ -24,12 +26,8 @@ jobs:
   - bash: |
       conda config --set always_yes yes --set changeps1 no
       conda info -a
-      conda create -n pygenometracks --yes -c conda-forge -c bioconda python=$(python.version) --file requirements.txt
+      conda create -n pygenometracks --yes -c conda-forge -c bioconda python=$(python.version) --file requirements_CI.txt
       source activate pygenometracks
-      conda install --yes -c conda-forge -c bioconda pytest flake8 pytest-xdist pytest-forked
-      conda install --yes -c conda-forge -c bioconda nose
-      conda install --yes pathlib
-      conda install --yes -c defaults -c conda-forge -c bioconda configparser
       python setup.py install
     displayName: installing dependencies
   - script: |
@@ -44,7 +42,7 @@ jobs:
 - job: 'OSX'
   timeoutInMinutes: 0
   pool:
-    vmImage: 'macOS-10.14'
+    vmImage: 'macOS-11'
   strategy:
     matrix:
       Python36:
@@ -53,21 +51,24 @@ jobs:
         python.version: '3.7'
       Python38:
         python.version: '3.8'
+      Python39:
+        python.version: '3.9'
 
   steps:
   - bash: |
       echo "##vso[task.prependpath]$CONDA/bin"
       hash -r
     displayName: Add conda to PATH
+
+  # On Hosted macOS, the agent user doesn't have ownership of Miniconda's installation directory/
+  # We need to take ownership if we want to update conda or install packages globally
+  - bash: sudo chown -R $USER $CONDA
+    displayName: Take ownership of conda installation
   - bash: |
       conda config --set always_yes yes --set changeps1 no
       conda info -a
-      conda create -n pygenometracks --yes -c conda-forge -c bioconda python=$(python.version) --file requirements.txt
+      conda create -n pygenometracks --yes -c conda-forge -c bioconda python=$(python.version) --file requirements_CI.txt
       source activate pygenometracks
-      conda install --yes -c conda-forge -c bioconda pytest flake8 pytest-xdist pytest-forked
-      conda install --yes -c conda-forge -c bioconda nose
-      conda install --yes pathlib
-      conda install --yes -c defaults -c conda-forge -c bioconda configparser
       python setup.py install
     displayName: installing dependencies
   - script: |

diff --git a/requirements_travis.txt → requirements_CI.txt b/requirements_travis.txt → requirements_CI.txt
@@ -8,4 +8,14 @@ pysam >=0.14
 gffutils >=0.9
 pybedtools >=0.8.1
 tqdm >=4.20
-
+# Below are dependencies for tests
+pytest
+pytest-xdist
+pytest-forked
+flake8
+nose
+pathlib
+configparser
+ghostscript
+coverage
+coverage-badge
diff --git a/test_locally.sh b/test_locally.sh
@@ -2,22 +2,21 @@
 
 source $(dirname $(dirname $(which conda)))/etc/profile.d/conda.sh
 
-for TRAVIS_PYTHON_VERSION in 3.6 3.7 3.8; do
-    conda create -n pgt_test_${TRAVIS_PYTHON_VERSION} --yes -c bioconda -c conda-forge python=$TRAVIS_PYTHON_VERSION --file requirements_travis.txt
+for TRAVIS_PYTHON_VERSION in 3.6 3.7 3.8 3.9; do
+    conda create -n pgt_test_${TRAVIS_PYTHON_VERSION} --yes -c bioconda -c conda-forge python=$TRAVIS_PYTHON_VERSION --file requirements_CI.txt
     conda activate pgt_test_${TRAVIS_PYTHON_VERSION}
-    conda install --yes -c conda-forge -c bioconda pytest ghostscript coverage coverage-badge
     python setup.py install
     coverage run -m py.test
     coverage html
     coverage-badge -f -o docs/coverage.svg
     conda deactivate
 done
 
-TRAVIS_PYTHON_VERSION=3.9
-conda create -n pgt_test_${TRAVIS_PYTHON_VERSION} --yes -c bioconda -c conda-forge python=$TRAVIS_PYTHON_VERSION
-conda activate pgt_test_${TRAVIS_PYTHON_VERSION}
-conda install --yes -c conda-forge -c bioconda numpy bedtools h5py pytest ghostscript
-pip install -r requirements_travis.txt
-python setup.py install
-py.test pygenometracks --doctest-modules
-conda deactivate
+# TRAVIS_PYTHON_VERSION=3.10
+# conda create -n pgt_test_${TRAVIS_PYTHON_VERSION} --yes -c bioconda -c conda-forge python=$TRAVIS_PYTHON_VERSION
+# conda activate pgt_test_${TRAVIS_PYTHON_VERSION}
+# conda install --yes -c conda-forge -c bioconda bedtools
+# pip install -r requirements_CI.txt
+# python setup.py install
+# py.test pygenometracks --doctest-modules
+# conda deactivate