#179 Make OpenStemmata a Python package

.github/workflows/pull_request.yml

@@ -16,7 +16,7 @@ jobs:
         python-version: 3.8
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install networkx lxml 
+        python -m pip install --upgrade pip pytest
+        pip install -e .
     - name: Tests 
-      run:  python ./tests/testthat.py 
+      run:  pytest

.github/workflows/transform.yml

@@ -1,18 +1,21 @@
 name: Transform
 
-on: 
-  push: 
+on:
+  push:
     branches:
       - main
     paths:
-      - 'data/**'
+      - 'src/openstemmata/data/**'
+
   workflow_dispatch: #Allows for manual triggering
 
 jobs:
   build:
     runs-on: ubuntu-latest
     env:
       GITHUB_TOKEN: ${{ secrets.TOKEN_PUSH }}
+      PACKAGE_PATH: src/openstemmata
+
     steps:
       - name: checkout repo content
         uses: actions/checkout@v2
@@ -27,10 +30,10 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install networkx lxml
+          pip install -r requirements.txt
       - name: Convert files
         run: |
-          for file in ./data/*/*/* ; do
+          for file in ./${{ PACKAGE_PATH }}/data/*/*/* ; do
             if [ "${file: -9}" == "stemma.gv" ] || [ "${file: -12}" == "metadata.txt" ] ; 
               then python ./tests/transformation.py ${file} ; 
             fi

.gitignore

@@ -1,2 +1,6 @@
 .Rhistory
-*pycache*
+*pycache*
+dist/
+OpenStemmata_database.egg-info
+.coverage
+.idea

CITATION.cff

@@ -1,6 +1,6 @@
 
 cff-version: 1.2.0
-message: "If you use this collection, please cite it as below (in adddition to references to the sources)."
+message: "If you use this collection, please cite it as below (in addition to references to the sources)."
 authors:
   - family-names: "Camps"
     given-names: "Jean-Baptiste"

MANIFEST.in

@@ -0,0 +1,3 @@
+graft src
+recursive-exclude __pycache__ *.py[cod]
+exclude tests/**

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"

requirements.txt

@@ -0,0 +1,2 @@
+networkx==3.3
+lxml==5.2.2

setup.cfg

@@ -0,0 +1,82 @@
+[metadata]
+name = openstemmata
+version = 0.1.0
+
+author =
+author_email =
+url='https://github.com/OpenStemmata/database',
+
+description = An open source collection of historical text genealogies, in forms of tree-like graphs (stemma) for a variety of languages.
+long_description = file: README.md
+long_description_content_type = text/markdown
+
+keywords =
+    manuscript
+    stemmatology
+license = CC-BY-SA-4.0 license
+license_files = LICENSE
+
+platforms = any
+classifiers =
+    Development Stats ::
+    Intended Audience :: Science/Research
+    Operating System :: OS Independent
+    License :: Other/Proprietary License (CC-BY License)
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
+
+[options]
+zip_safe = False
+packages = find:
+package_dir =
+    =src
+install_requires =
+    networkx
+    lxml
+include_package_data = True
+
+
+;include_dirs=[]
+
+[options.packages.find]
+where = src
+exclude =
+    test*
+
+[options.package_data]
+opentstemmata =
+    data/*
+    examples/*
+    schema/*
+
+;[testimports]
+;deps =
+;    pytest
+;    pytest-cov
+;
+;[test-env]
+;deps =
+;    {[testimports]deps}
+;commands =
+;    pytest {posargs}
+;
+;[options.extras_require]  # in setup.cfg
+;test =
+;    pytest
+;    pytest-cov
+;
+;[tool:pytest]
+;addopts = --cov
+;testpaths =
+;    tests
+;
+;[coverage:run]
+;source=openstemmata_database
+;
+;[coverage:report]
+;show_missing = True
+

setup.py

@@ -0,0 +1,3 @@
+from setuptools import setup
+
+setup()

src/openstemmata/__init__.py

@@ -0,0 +1,3 @@
+import os
+
+PACK_DIR = os.path.abspath(os.path.dirname(__file__))