Merge pull request #168 from bigbio/ypriverol-patch-1

OLS refactoring.

.github/workflows/conda-build.yml

@@ -0,0 +1,60 @@
+name: Conda Build
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: true
+        python-version: 3.8
+        channels: conda-forge,defaults,bioconda
+
+    - name: Create conda environment
+      run: conda env create -f environment.yml
+
+    - name: Activate conda environment
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda activate sdrf-pipelines
+      shell: bash
+
+    - name: Install conda-build
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda activate sdrf-pipelines
+        conda install -n sdrf-pipelines conda-build anaconda-client
+      shell: bash -l {0}
+
+    - name: Activate conda environment and build package
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda activate sdrf-pipelines
+        conda build recipe
+      shell: bash -l {0}
+
+    - name: Install the built package
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda activate sdrf-pipelines
+        conda install --use-local sdrf-pipelines
+      shell: bash -l {0}
+
+    - name: Test the installed package
+      run: |
+        conda activate sdrf-pipelines
+        parse_sdrf --help
+      shell: bash -l {0}
+
+    - name: Test other commands
+      run: |
+        conda activate sdrf-pipelines
+        parse_sdrf validate-sdrf --sdrf_file tests/data/reference/PDC000126/PDC000126.sdrf.tsv --check_ms
+      shell: bash -l {0}

environment.yml

@@ -0,0 +1,20 @@
+name: sdrf-pipelines
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python=3.8
+  - conda-build
+  - anaconda-client
+  - pandas
+  - click
+  - requests
+  - pyyaml
+  - numpy
+  - defusedxml
+  - pyarrow
+  - python-duckdb
+  - rdflib
+  - pandas_schema
+

recipe/meta.yaml

@@ -0,0 +1,49 @@
+# recipe/meta.yaml
+package:
+  name: sdrf-pipelines
+  version: "0.0.27"
+
+source:
+  path: ../
+
+build:
+  noarch: python
+  entry_points:
+      - parse_sdrf = sdrf_pipelines.parse_sdrf:main
+  script:
+    - {{ PYTHON }} -m pip install --no-deps --ignore-installed .
+
+requirements:
+  host:
+    - pip
+    - python >=3.5
+  run:
+    - click
+    - requests
+    - pandas
+    - pandas_schema
+    - python >=3.5
+    - pyaml
+    - defusedxml
+    - pytest
+    - duckdb
+    - rdflib
+    - pyarrow
+
+test:
+  imports:
+    - sdrf_pipelines
+    - sdrf_pipelines.openms
+    - sdrf_pipelines.sdrf
+    - sdrf_pipelines.utils
+    - sdrf_pipelines.ols
+  commands:
+    - parse_sdrf --help
+
+about:
+  home: "https://github.com/bigbio/sdrf-pipelines"
+  license: Apache 2
+  ##license_file: LICENSE ## patch is applied upstream, next version will have it
+  summary: "Translate, convert SDRF to configuration pipelines"
+  doc_url: "https://github.com/bigbio/sdrf-pipelines"
+  dev_url: "https://github.com/bigbio/sdrf-pipelines"

requirements.txt

@@ -9,4 +9,7 @@ pandas_schema
 requests
 pyyaml
 numpy
-defusedxml
+defusedxml
+pyarrow
+duckdb
+rdflib

sdrf_pipelines/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.26"
+__version__ = "0.0.27"