Cookiecutting - modify files v2

.codecov.yml

@@ -1,2 +1,37 @@
+# codecov can find this file anywhere in the repo, so we don't need to clutter
+# the root folder.
+#comment: false
+
 fixes:
   - ".*/site-packages/::src/"
+
+codecov:
+  notify:
+    require_ci_to_pass: no
+
+coverage:
+  status:
+    patch:
+      default:
+        target: '70'
+        if_no_uploads: error
+        if_not_found: success
+        if_ci_failed: failure
+    project:
+      default: false
+      library:
+        target: auto
+        if_no_uploads: error
+        if_not_found: success
+        if_ci_failed: error
+        paths: '!*/tests/.*'
+
+      tests:
+        target: 97.9%
+        paths: '*/tests/.*'
+        if_not_found: success
+
+flags:
+  tests:
+    paths:
+      - tests/

.coveragerc

@@ -1,6 +1,16 @@
-# Configuration of the coverage.py tool for reporting test coverage.
-
+[run]
+source =
+    diffpy.pdffit2
+omit =
+    ## exclude debug.py from codecov report
+    */tests/debug.py
 [report]
+omit =
+    */python?.?/*
+    */site-packages/nose/*
+    # ignore _version.py and versioneer.py
+    .*version.*
+    *_version.py
 # RE patterns for lines to be excluded from consideration.
 exclude_lines =
     ## Have to re-enable the standard pragma
@@ -13,10 +23,4 @@ exclude_lines =
     ## Don't complain if non-runnable code isn't run:
     ^[ ]*@unittest.skip\b
     ^[ ]{4}unittest.main()
-    if __name__ == .__main__.:
-
-
-[run]
-omit =
-    ## exclude debug.py from codecov report
-    */tests/debug.py
+    if __name__ == '__main__':

.github/workflows/main.yml

@@ -44,7 +44,7 @@ jobs:
           conda activate test
           conda install --file requirements/run.txt
           conda install --file requirements/test.txt
-          pip install -e .
+          pip install .
       - name: Validate diffpy.pdffit2
         shell: bash -l {0}
         run: |

MANIFEST.in

@@ -1,20 +1,28 @@
-recursive-include diffpy *
-recursive-exclude diffpy *.py[co] *.so
-recursive-include libpdffit2 *.[ch]*
-recursive-include pdffit2module *.[ch]*
-recursive-include examples *
-include AUTHORS.txt LICENSE*.txt README*
-include Makefile
-prune libpdffit2/tests
+recursive-include src/diffpy *
+recursive-exclude src/diffpy *.py[co] *.so
+recursive-include docs *.rst conf.py Makefile make.bat
+
+recursive-include src/extensions/libpdffit2 *.[ch]*
+recursive-include src/extensions/pdffit2module *.[ch]*
+recursive-include src/examples *
+include AUTHORS.rst
+include diffpy.pdffit2/version.py
+include LICENSE.rst
+include README.rst
+include requirements/
+prune src/extensions/libpdffit2/tests
 global-exclude .gitattributes .gitignore .gitarchive.cfg
 global-exclude .DS_Store
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+# If including data files in the package, add them like:
+# include path/to/data_file
 
 # Avoid user content in setup.cfg to make distribution reproducible.
 exclude setup.cfg
 
 # Exclude git-tracked files spuriously added by setuptools_scm
 exclude .coveragerc
-exclude .travis*
-prune conda-recipe
 prune devutils
 prune doc