WIP branch to test updated dependencies

- this branch can be rebased on dev-ssciwr as more tests are added there
- allow pytohn 3.6-3.9 in setup.cfg
- use dev-ssciwr branch of pbiotools
  - temporarily add all of its conda deps to our environment here
  - then install using --no-deps to avoid bringing in pypi dependencies
  - once pbiotools is published on bioconda can switch to using that & remove these conda deps
- use bioconda for all other rp-bp deps
  - currently no version pins except pystan < 3
  - this is hopefully a similar setup to the eventual bioconda recipe for rp-bp
- add macos to CI now that flexbar is available for mac on bioconda

.github/workflows/ci.yml

@@ -12,24 +12,24 @@ on: push
 
 jobs:
   install-and-test:
-    name: ${{matrix.os}}
     runs-on: ${{matrix.os}}
     defaults:
       run:
         shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-latest]
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.6", "3.7", "3.8", "3.9"]
     steps:
       - uses: actions/checkout@v3
-      - name: Create rpbp conda environment
+      - name: Create rpbp-dev conda environment
         uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: 3.6
+          python-version: ${{ matrix.python-version }}
           auto-update-conda: true
           auto-activate-base: false
-          activate-environment: rpbp
+          activate-environment: rpbp-dev
           environment-file: environment.yml
       - name: Display conda env info
         run: |
@@ -38,6 +38,8 @@ jobs:
           conda config --show-sources
           conda config --show
           printenv | sort
+      - name: Install pbiotools
+        run: pip install git+https://github.com/dieterich-lab/pbiotools.git@dev-ssciwr --no-deps --verbose
       - name: Install rp-bp
         run: pip install . --verbose
       - name: Run tests

environment.yml

@@ -1,27 +1,43 @@
-name: rpbp
+name: rpbp-dev
 channels:
   - defaults
   - conda-forge
   - bioconda
 dependencies:
-  - python=3.6
-  - flexbar=3.5.0
-  - bowtie2=2.3.0
+  - python
+  - flexbar
+  - bowtie2
   - pip
   - star
-  - samtools=1.7
-  - openssl=1.0 # pin old openssl version to fix "error while loading shared libraries: libcrypto.so.1.0.0"
-  - pip:
-      - setuptools>=38.3.0
-      - numpy>=1.16,<1.17
-      - scipy==1.2.1 # Statsmodels 0.9/Scipy 1.3.0 incompatibility
-      - statsmodels==0.9.0
-      - pandas==0.24.0
-      - pystan==2.19.0.0
-      - joblib==0.13.2
-      - biopython==1.73
-      - git+https://github.com/dieterich-lab/pbiotools.git@dev-ssciwr#egg=pbiotools
-      - pysam==0.15.2 # with Samtools-1.7
-      - pyyaml==5.4
-      - pytest
-      - pytest-cov
+  - samtools
+  - pysam
+  - pyyaml
+  - pystan <3
+  - biopython
+  - scipy
+  - statsmodels
+  - pandas
+  - numpy
+  - joblib
+  - pytest
+  - pytest-cov
+  # pbiotools conda dependencies:
+  - dask
+  - scikit-learn
+  - appdirs
+  - tqdm
+  - mygene
+  - openpyxl
+  - fastparquet
+  - more-itertools
+  - matplotlib-base
+  - matplotlib-venn
+  - seaborn
+  - pysam
+  - pybedtools
+  - biopython
+  - pyensembl
+  - pystan <3
+  #- pip:
+  # can't do --no-deps inside here apparently...
+#      - git+https://github.com/dieterich-lab/pybiotools.git@dev-ssciwr

setup.cfg

@@ -25,7 +25,7 @@ packages = find:
 # see requirements.txt
 install_requires =
     pbio
-python_requires = >=3.6,<3.7.0a0
+python_requires = >=3.6,<3.10.0a0
 # Add entries to MANIFEST.in
 include_package_data = True
 zip_safe = False