fixed sdist creation

Author: siebrenf

.codeclimate.yml

@@ -26,7 +26,7 @@ exclude_patterns:
   - "*.txt"
   - "*.yml"
   - "*.yaml"
-  - "build.py"
+  - "custom_build.py"
   - "COPYING"
   - "**/__*"
   - "**/*.c"

.gitignore

@@ -14,6 +14,7 @@ gimmemotifs/included_tools/
 gimmemotifs.egg-info/
 src/
 test_py/
+venv/
 
 # tests
 .pytest_cache/

build.py custom_build.pybuild.py renamed to custom_build.py

@@ -40,7 +40,7 @@ git flow release start ${new_version}
 
 ```shell
 pip wheel -w dist --no-deps --no-cache-dir --use-pep517 -v .
-mamba env create -n test -f requirements.yaml
+mamba env create --force -n test -f requirements.yaml
 mamba activate test
 pip install --no-deps --no-cache-dir --use-pep517 -v dist/gimmemotifs*.whl
 
@@ -52,14 +52,23 @@ pytest -vvv --disable-pytest-warnings
 
 ## 5. Upload to pypi testing server
 
+For more info, see https://packaging.python.org/en/latest/tutorials/packaging-projects/#generating-distribution-archives
+
 ```
-# Check for warnings or errors
-$ python setup.py check -r -s
-# Create distribution
-$ python setup.py sdist
+# Create the source distribution
+$ python3 -m pip install --upgrade build
+$ python3 -m build
+
+# Test the source distribution
+$ pip install --no-deps --no-cache-dir --use-pep517 -v dist/gimmemotifs*.tar.gz
+$ rm ~/.config/gimmemotifs/gimmemotifs.cfg
+$ gimme -h
+$ pytest -vvv --disable-pytest-warnings
+
 # Upload to pypi testing server
-$ twine upload -r testpypi dist/gimmemotifs-${version}.tar.gz
-``` 
+$ python3 -m pip install --upgrade twine
+$ python3 -m twine upload --repository testpypi dist/*
+```
 
 ## 6. Finish release
 
@@ -77,8 +86,7 @@ git push --follow-tags origin develop master
 ## 8. Upload to PyPi.
 
 ```shell
-python setup.py sdist
-twine upload dist/gimmemotifs-${new_version}.tar.gz
+twine upload dist/*
 ```
 
 ## 9. Finalize the release on Github.

docs/release_checklist.md

@@ -105,28 +105,33 @@ packages = [
     "gimmemotifs.motif",
     "gimmemotifs.scanner",
     "gimmemotifs.tools",
+
+    # only needed in the sdist
+    "src",
+    "src.AMD",
+    "src.BioProspector",
+    "src.ChIPMunk",
+    "src.HMS",
+    "src.Improbizer",
+    "src.MDmodule",
+    "src.MotifSampler",
+    "src.posmo",
 ]
 ext-modules = [
     {name = "gimmemotifs.c_metrics", sources=["gimmemotifs/c_metrics.c"]},
 ]
+py-modules = ["custom_build"]  # only needed in the sdist
 
 [tool.setuptools.package-data]
-data = [
-    "bg/*",
-    "cfg/*",
-    "examples/*",
-    "motif_databases/*",
-    "score_dists/*",
-    "templates/*",
-    "templates.sortable/*",
-]
+data = ["**"]
+src = ["**"]
 
 [tool.setuptools.exclude-package-data]
 gimmemotifs = ["*__pycache__*"]
 data = ["*__pycache__*"]
 
 [tool.setuptools.cmdclass]
-build_py = "build.custom_build_py"  # adds the motif prediction tools
+build_py = "custom_build.custom_build_py"  # adds the motif prediction tools
 # options for automatic cleanup of editable uninstallation:
 # editable_wheel = "build.custom_editable_wheel"
 # egg_info = "build.custom_egg_info"

pyproject.toml

@@ -6,7 +6,7 @@
 def test_black_formatting():
     try:
         sp.check_output(
-            "black --check gimmemotifs/ scripts/ test/ build.py",
+            "black --check gimmemotifs/ scripts/ test/ custom_build.py",
             stderr=sp.STDOUT,
             shell=True,
         )
@@ -20,7 +20,7 @@ def test_black_formatting():
 def test_isort_formatting():
     try:
         sp.check_output(
-            "isort --check gimmemotifs/ scripts/ test/ build.py",
+            "isort --check gimmemotifs/ scripts/ test/ custom_build.py",
             stderr=sp.STDOUT,
             shell=True,
         )