New way of initializing bedstat

.github/workflows/python-publish.yml

@@ -0,0 +1,31 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

.github/workflows/test-pipeline.yml

@@ -2,15 +2,15 @@ name: Test bedstat pipeline
 
 on:
   push:
-    branches: [master, dev]
+    branches: [master, dev, dev_alex]
   pull_request:
     branches: [master, dev]
 
 jobs:
   pytest:
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.8]
         os: [ubuntu-latest] # can't use macOS when using service containers or container jobs
         r: [release]
     runs-on: ${{ matrix.os }}
@@ -46,25 +46,27 @@ jobs:
         sudo apt-get update
         sudo apt-get install libcurl4-openssl-dev
 
-    - uses: r-lib/actions/setup-r@master
-      with:
-        r-version: ${{ matrix.r }}
+    - name: Install package
+      run: python -m pip install .
 
-    - name: Install R dependancies
-      run: Rscript scripts/installRdeps.R
+    - name: Run pytest tests
+      run: pytest tests -x -vv
 
-    - name: Run pipeline
-      run: looper run -p local tests/data/bedstat_config.yaml
+      #    - uses: r-lib/actions/setup-r@master
+#      with:
+#        r-version: ${{ matrix.r }}
+#
+#    - name: Install R dependancies
+#      run: Rscript scripts/installRdeps.R
 
-    - name: Test plots exist
-      run: |
-        if ls $GITHUB_WORKSPACE/outputs/bedstat_output/a6a08126cb6f4b1953ba0ec8675df85a/test_hg38*.png 1> /dev/null 2>&1; then
-          echo "SUCCESS";
-        else
-          echo "ERROR: files do not exist: $GITHUB_WORKSPACE/outputs/bedstat_output/a6a08126cb6f4b1953ba0ec8675df85a/test_hg38*.png";
-          exit 1
-        fi
-
-    - name: Test record in PostgreSQL
-      run: |
-        echo "from bbconf import BedBaseConf; from bbconf.const import *; bbc = BedBaseConf('$GITHUB_WORKSPACE/tests/data/config_min.yaml'); assert bbc.bed.record_count == 1, 'Number of records in the bedfiles table not equal 1'" | python3 -
+#    - name: Run pipeline
+#      run: looper run -p local tests/data/bedstat_config.yaml
+#
+#    - name: Test plots exist
+#      run: |
+#        if ls $GITHUB_WORKSPACE/outputs/bedstat_output/a6a08126cb6f4b1953ba0ec8675df85a/test_hg38*.png 1> /dev/null 2>&1; then
+#          echo "SUCCESS";
+#        else
+#          echo "ERROR: files do not exist: $GITHUB_WORKSPACE/outputs/bedstat_output/a6a08126cb6f4b1953ba0ec8675df85a/test_hg38*.png";
+#          exit 1
+#        fi

LICENSE.txt

@@ -0,0 +1,9 @@
+Copyright 2017 Nathan Sheffield
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -0,0 +1,6 @@
+include README.md
+include requirements/*
+include schemas/*
+include bedstat/scripts/*
+include bedstat/tools/regionstat.R
+include bedstat/pep_schema.yaml

README.md

@@ -30,7 +30,7 @@ The above command will build the csv file looper needs to run the pipeline on al
 
 ### 1. Validate your PEP with [`eido`](https://github.com/pepkit/eido)
 
-The input PEP can be validated against the [JSON schema in this repository](pep_schema.yaml). This ensures the PEP consists of all required attributes to run `bedstat` pipeline.
+The input PEP can be validated against the [JSON schema in this repository](schemas/pep_schema.yaml). This ensures the PEP consists of all required attributes to run `bedstat` pipeline.
 
 ```
 eido validate <path/to/pep> -s https://schema.databio.org/pipelines/bedstat.yaml
@@ -58,7 +58,7 @@ The data loaded into PostgreSQL should persist between PostgreSQL invocations, o
 
 ## Additional dependencies
 
-[regionstat.R](tools/regionstat.R) script is used to calculate the bed file statistics, so the pipeline also depends on several R packages:
+[regionstat.R](bedstat/tools/regionstat.R) script is used to calculate the bed file statistics, so the pipeline also depends on several R packages:
 
 * `R.utils`
 * `BiocManager`
@@ -71,7 +71,7 @@ The data loaded into PostgreSQL should persist between PostgreSQL invocations, o
 * `BSgenome.<organim>.UCSC.<genome>` *depending on the genome used* 
 * `LOLA`
 
-you can use [installRdeps.R](scripts/installRdeps.R) helper script to easily install the required packages:
+you can use [installRdeps.R](bedstat/scripts/installRdeps.R) helper script to easily install the required packages:
 
 ```
 Rscript scripts/installRdeps.R

bedstat/__init__.py

@@ -0,0 +1,3 @@
+""" Package-level data """
+from .bedstat import *
+from ._version import __version__

bedstat/_version.py

@@ -0,0 +1 @@
+__version__ = "0.1.0"