blacken, fix github actions, badges

.github/workflows/python-package.yml

@@ -6,8 +6,6 @@ on:
   pull_request:
     branches: [ "master" ]
 
-#
-
 jobs:
   build:
 
@@ -23,14 +21,10 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+        allow-prereleases: true
     - name: Install dependencies
       run: |
-        python -m venv .venv
-        source .venv/bin/activate
-        pip install --upgrade pip
-        pip install pytest coverage[toml] tox
-        pip install -e .
-    - name: Run tox
+        make install
+    - name: Run tests
       run: |
-        source .venv/bin/activate
-        tox -e py
+        make test

Makefile

@@ -1,6 +1,7 @@
 .PHONY: lint test dist upload docs
 
-BIN=.venv/bin/
+ENV=.venv
+BIN=$(ENV)/bin/
 DIRS=src/ tests/unit/ docs/ scripts/ # tests/performance/
 BROWSER=firefox
 PYTEST=pytest --doctest-modules --doctest-glob="*.rst" --doctest-ignore-import-errors
@@ -20,54 +21,54 @@ mypy:
 	-$(BIN)mypy $(DIRS)
 
 doc8:
-	-doc8 README.rst
+	-$(BIN)doc8 README.rst
 
 pydocstyle:
-	$(BIN)pydocstyle src/
+	-$(BIN)pydocstyle src/
 
 lint: black blackdoc pylint mypy pydocstyle
 
 test:
-	$(BIN)python3 -m $(PYTEST) src/ tests/ docs/ README.rst
+	$(BIN)python -m $(PYTEST) src/ tests/ docs/ README.rst
 
 test-performance:
-	$(BIN)python3 -m $(PYTEST) --performance tests/performance/
+	$(BIN)python -m $(PYTEST) --performance tests/performance/
 
 coverage:
 	$(BIN)coverage erase
 	$(BIN)coverage run --branch --source=src -m $(PYTEST) tests/
 	$(BIN)coverage run --append --branch --source=src -m $(PYTEST) --debug-mode tests/
-	$(BIN)coverage report
 	$(BIN)coverage html
 	$(BROWSER) htmlcov/index.html
+	$(BIN)coverage json -o - | $(BIN)python tests/make_coverage_badge.py > docs/_images/badge-coverage.svg
 
 profile:
-	$(BIN)python3 -O -m scripts.profile
+	$(BIN)python -O -m scripts.profile
 
 docs:
-	cd docs; make html
-
-badges: coverage
-	$(BIN)python docs/make_badges.py
+	cd docs; make SPHINXBUILD='../$(BIN)python -msphinx' html
 
 tox:
 	$(BIN)tox
 
-dist: clean test coverage badges
-	$(BIN)python3 -m build
+dist: clean tox coverage docs
+	$(BIN)python -m build
 	$(BIN)twine check dist/*
 
 upload: dist
 	$(BIN)twine check dist/*
 	$(BIN)twine upload dist/*
 
 install:
-	$(BIN)pip3 install --force-reinstall -e .
+	python -m venv --clear $(ENV)
+	$(BIN)pip install -r requirements-dev.txt
+	$(BIN)pip install --force-reinstall -e .
 
 uninstall:
-	$(BIN)pip3 uninstall super_collator
+	$(BIN)pip uninstall super_collator
 
 clean:
-	-rm -rf dist build *.egg-info
+	-rm -rf dist build htmlcov .mypy_cache .pytest_cache .tox *.egg-info
+	-rm docs/_images/badge*.svg
 	-rm *~ .*~ pylintgraph.dot
 	-find . -name __pycache__ -type d -exec rm -r "{}" \;

README.rst

@@ -2,17 +2,17 @@
 Super Collator
 ==============
 
-.. |py39| image:: docs/_images/tox-py39.svg
+.. |py39| image:: docs/_images/badge-py39.svg
 
-.. |py310| image:: docs/_images/tox-py310.svg
+.. |py310| image:: docs/_images/badge-py310.svg
 
-.. |py311| image:: docs/_images/tox-py311.svg
+.. |py311| image:: docs/_images/badge-py311.svg
 
-.. |py312| image:: docs/_images/tox-py312.svg
+.. |py312| image:: docs/_images/badge-py312.svg
 
-.. |pypy39| image:: docs/_images/tox-pypy39.svg
+.. |pypy39| image:: docs/_images/badge-pypy39.svg
 
-.. |coverage| image:: docs/_images/coverage.svg
+.. |coverage| image:: docs/_images/badge-coverage.svg
 
 |py39| |py310| |py311| |py312| |pypy39| |coverage|
 

docs/examples.rst

@@ -24,7 +24,9 @@ Align two strings with relaxed spelling using N-Grams:
    >>> b = [NGrams(s).load(s, 3) for s in b.split()]
    >>>
    >>> a, b, score = aligner.align(a, b, NGrams.similarity, lambda: NGrams("-"))
-   >>> print(to_table(list(map(str, a)), list(map(str, b))))  # doctest: +NORMALIZE_WHITESPACE
+   >>> print(
+   ...     to_table(list(map(str, a)), list(map(str, b)))
+   ... )  # doctest: +NORMALIZE_WHITESPACE
    -   Lorem   ipsum -    dollar -   amat -           adipiscing elit
    qui dolorem ipsum quia dolor  sit amet consectetur adipisci   velit
 
@@ -45,9 +47,11 @@ Multiple alignment: We repeatedly align two lists of NGrams against each other.
    ...             if score > sim:
    ...                 sim = score
    ...     return sim
+   ...
    >>>
    >>> def merge(aa, bb):
    ...     return [a + b for a, b in zip(aa, bb)]
+   ...
    >>>
    >>> aligner = Aligner(-1.0, -0.5, -0.5)
    >>> a = "qui dolorem ipsum quia dolor sit amet consectetur adipisci velit"
@@ -58,12 +62,18 @@ Multiple alignment: We repeatedly align two lists of NGrams against each other.
    >>> b = [[NGrams(s).load(s, 2)] for s in b.split()]
    >>> c = [[NGrams(s).load(s, 2)] for s in c.split()]
    >>>
-   >>> a,  b, score = aligner.align(a,  b, similarity, lambda: [NGrams("-")], lambda: [NGrams("-")])
+   >>> a, b, score = aligner.align(
+   ...     a, b, similarity, lambda: [NGrams("-")], lambda: [NGrams("-")]
+   ... )
    >>> ab = merge(a, b)
-   >>> ab, c, score = aligner.align(ab, c, similarity, lambda: [NGrams("-")] * 2, lambda: [NGrams("-")])
+   >>> ab, c, score = aligner.align(
+   ...     ab, c, similarity, lambda: [NGrams("-")] * 2, lambda: [NGrams("-")]
+   ... )
    >>> abc = merge(ab, c)
    >>>
-   >>> print(to_table(*zip(*[[t.user_data for t in nn] for nn in abc])))  # doctest: +NORMALIZE_WHITESPACE
+   >>> print(
+   ...     to_table(*zip(*[[t.user_data for t in nn] for nn in abc]))
+   ... )  # doctest: +NORMALIZE_WHITESPACE
    qui dolorem ipsum quia dolor  sit amet consectetur adipisci   velit
    -   Lorem   ipsum -    -      -   -    -           adipiscing -
    -   Lorem   -     -    dollar -   amat -           -          elit
@@ -87,6 +97,7 @@ Align two sentences using their part-of-speech tags only:
    ...     @staticmethod
    ...     def similarity(a, b):
    ...         return 1.0 if a.pos == b.pos else 0.0
+   ...
    >>>
    >>> aligner = Aligner()
    >>> a = "it/PRP was/VBD a/DT dark/JJ and/CC stormy/JJ night/NN"
@@ -96,6 +107,8 @@ Align two sentences using their part-of-speech tags only:
    >>> b = [PosToken(*s.split("/")) for s in b.split()]
    >>>
    >>> c, d, score = aligner.align(a, b, PosToken.similarity, lambda: PosToken("-", ""))
-   >>> print(to_table(list(map(str, c)), list(map(str, d))))  # doctest: +NORMALIZE_WHITESPACE
+   >>> print(
+   ...     to_table(list(map(str, c)), list(map(str, d)))
+   ... )  # doctest: +NORMALIZE_WHITESPACE
    it was a dark and stormy night
    it is  a fine -   -      day

pyproject.toml

@@ -17,6 +17,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Text Processing :: Indexing",
     "Topic :: Text Processing :: Linguistic",
 ]
@@ -81,9 +82,12 @@ legacy_tox_ini = """
 [tox]
 isolated_build = True
 envlist = pypy39,py39,py310,py311,py312
+skip_missing_interpreters = True
 
 [testenv]
 allowlist_externals = make
-deps = pytest
-commands = make test
+deps =
+  pytest
+  requests
+commands = make BIN= test
 """

requirements-dev.txt

@@ -3,14 +3,14 @@ blackdoc
 build
 coverage[toml]
 hatchling
-lxml
 mypy
-pip
 pydocstyle
 pylint
 pytest
+requests
 sphinx
 sphinx-rtd-theme
 toml
 tox
+types-requests
 twine

src/super_collator/aligner.py

@@ -57,7 +57,9 @@ def html(self) -> str:
                 emph[2] = True
         klass: List
         cells = []
-        for val, klass, em in zip((self.m, self.p, self.q), (["d"], ["p"], ["q"]), emph):  # type: ignore
+        for val, klass, em in zip(
+            (self.m, self.p, self.q), (["d"], ["p"], ["q"]), emph
+        ):  # type: ignore
             klass.append("inner")
             if em:
                 klass.append("em")
@@ -142,7 +144,8 @@ def align(
 
         :param seq_a: the first sequence to align
         :param seq_b: the second sequence to align
-        :param similarity: a callable that returns the similarity of two members of seq_a and seq_b
+        :param similarity: a callable that returns the similarity of two members
+            of seq_a and seq_b
         :param gap_a: insert gap_a() for a gap in sequence a. None inserts None.
         :param gap_b: insert gap_b() for a gap in sequence b. None inserts gap_a().
         :return: the aligned sequences and the score
@@ -162,7 +165,8 @@ def align_debug(
 
         :param seq_a: the first sequence to align
         :param seq_b: the second sequence to align
-        :param similarity: a callable that returns the similarity of two members of seq_a and seq_b
+        :param similarity: a callable that returns the similarity of two members
+            of seq_a and seq_b
         :param gap_a: insert gap_a() for a gap in sequence a. None inserts None.
         :param gap_b: insert gap_b() for a gap in sequence b. None inserts gap_a().
         :param debug: calculate debug information if True, debug info wastes memory
@@ -210,7 +214,6 @@ def align_debug(
 
         # Score the matrix
         for i, a in enumerate(seq_a, start=1):
-
             # add new back_row to back_matrix
             this_back_row = []
             back_matrix.append(this_back_row)

tests/conftest.py

@@ -2,9 +2,10 @@
 import sys
 
 import pytest
+import requests
 
 class DebugAction(argparse.Action):
-    """Turn on debug mode for coverage tests."""
+    """This action turns on the DEBUG flags so we get coverage of the debug code."""
     def __init__(self, option_strings, dest, nargs=None, **kwargs):
         if nargs is not None:
             raise ValueError("nargs not allowed")
@@ -16,11 +17,37 @@ def __call__(self, parser, namespace, values, option_string=None):
             pass
 
 
-
 def pytest_addoption(parser):
     parser.addoption(
         "--performance", action="store_true", help="run performance tests"
     )
     parser.addoption(
         "--debug-mode", action=DebugAction, help="turn on DEBUG mode while testing"
     )
+
+def pytest_sessionfinish(session, exitstatus):
+    """Hook called after whole test run finished, right before returning
+    the exit status to the system."""
+
+    DESTDIR = "docs/"  # physical
+
+    if sys.implementation.name == "pypy":
+        py = "pypy"
+    else:
+        py = "py"
+    if exitstatus == 0:
+        status = "passing"
+        color = "success"
+    else:
+        status = "failed"
+        color = "critical"
+    name = f"{py}{sys.version_info.major}{sys.version_info.minor}"
+
+    badge = requests.get(
+        f"https://img.shields.io/badge/{name}-{status}-{color}"
+    ).text
+
+    filename = f"_images/badge-{name}.svg"
+    with open(f"{DESTDIR}{filename}", "w") as dest:
+        dest.write(badge)
+        print(f"{filename}")

tests/make_coverage_badge.py

@@ -0,0 +1,24 @@
+#!python3
+
+import json
+import sys
+
+import requests
+
+# shields_io_colors = ["success", "important", "critical", "informational", "inactive"]
+
+if __name__ == "__main__":
+    j = json.load(sys.stdin)
+    coverage = j["totals"]["percent_covered_display"]
+
+    cov = int(coverage)
+    if cov > 95:
+        color = "success"
+    elif cov > 75:
+        color = "important"
+    else:
+        color = "critical"
+
+    print(requests.get(
+        f"https://img.shields.io/badge/coverage-{cov}%-{color}"
+    ).text)