Ci updates (#7)

* updated Github Actions and Codecov badges in README.md

* used black to reformat all files outside of src folder

* added Codecov report upload to CI.yaml

.github/workflows/CI.yaml

@@ -62,3 +62,9 @@ jobs:
           file: ./coverage.xml
           flags: unittests
           name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/[email protected]
+        env:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: choderalab/missense-kinase-toolkit

README.md

@@ -1,8 +1,8 @@
 missense-kinase-toolkit
 ==============================
 [//]: # (Badges)
-[![GitHub Actions Build Status](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/missense_kinase_toolkit/workflows/CI/badge.svg)](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/missense_kinase_toolkit/actions?query=workflow%3ACI)
-[![codecov](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/missense-kinase-toolkit/branch/main/graph/badge.svg)](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/missense-kinase-toolkit/branch/main)
+[![GitHub Actions Build Status](https://github.com/choderalab/missense_kinase_toolkit/workflows/CI/badge.svg)](https://github.com/choderalab/missense_kinase_toolkit/actions?query=workflow%3ACI)
+[![codecov](https://codecov.io/gh/choderalab/missense-kinase-toolkit/branch/main/graph/badge.svg)](https://codecov.io/gh/choderalab/missense-kinase-toolkit/branch/main)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/choderalab/missense-kinase-toolkit/main.svg?badge_token=dufHMzu_RH2VGGToCgvtcQ)](https://results.pre-commit.ci/latest/github/choderalab/missense-kinase-toolkit/main?badge_token=dufHMzu_RH2VGGToCgvtcQ)
 
 

devtools/scripts/create_conda_env.py

@@ -6,9 +6,11 @@
 import subprocess as sp
 from tempfile import TemporaryDirectory
 from contextlib import contextmanager
+
 # YAML imports
 try:
     import yaml  # PyYAML
+
     loader = yaml.safe_load
 except ImportError:
     try:
@@ -17,19 +19,30 @@
         try:
             # Load Ruamel YAML from the base conda environment
             from importlib import util as import_util
-            CONDA_BIN = os.path.dirname(os.environ['CONDA_EXE'])
-            ruamel_yaml_path = glob.glob(os.path.join(CONDA_BIN, '..',
-                                                      'lib', 'python*.*', 'site-packages',
-                                                      'ruamel_yaml', '__init__.py'))[0]
+
+            CONDA_BIN = os.path.dirname(os.environ["CONDA_EXE"])
+            ruamel_yaml_path = glob.glob(
+                os.path.join(
+                    CONDA_BIN,
+                    "..",
+                    "lib",
+                    "python*.*",
+                    "site-packages",
+                    "ruamel_yaml",
+                    "__init__.py",
+                )
+            )[0]
             # Based on importlib example, but only needs to load_module since its the whole package, not just
             # a module
-            spec = import_util.spec_from_file_location('ruamel_yaml', ruamel_yaml_path)
+            spec = import_util.spec_from_file_location("ruamel_yaml", ruamel_yaml_path)
             yaml = spec.loader.load_module()
         except (KeyError, ImportError, IndexError):
-            raise ImportError("No YAML parser could be found in this or the conda environment. "
-                              "Could not find PyYAML or Ruamel YAML in the current environment, "
-                              "AND could not find Ruamel YAML in the base conda environment through CONDA_EXE path. "
-                              "Environment not created!")
+            raise ImportError(
+                "No YAML parser could be found in this or the conda environment. "
+                "Could not find PyYAML or Ruamel YAML in the current environment, "
+                "AND could not find Ruamel YAML in the base conda environment through CONDA_EXE path. "
+                "Environment not created!"
+            )
     loader = yaml.YAML(typ="safe").load  # typ="safe" avoids odd typing on output
 
 
@@ -46,13 +59,16 @@ def temp_cd():
 
 
 # Args
-parser = argparse.ArgumentParser(description='Creates a conda environment from file for a given Python version.')
-parser.add_argument('-n', '--name', type=str,
-                    help='The name of the created Python environment')
-parser.add_argument('-p', '--python', type=str,
-                    help='The version of the created Python environment')
-parser.add_argument('conda_file',
-                    help='The file for the created Python environment')
+parser = argparse.ArgumentParser(
+    description="Creates a conda environment from file for a given Python version."
+)
+parser.add_argument(
+    "-n", "--name", type=str, help="The name of the created Python environment"
+)
+parser.add_argument(
+    "-p", "--python", type=str, help="The version of the created Python environment"
+)
+parser.add_argument("conda_file", help="The file for the created Python environment")
 
 args = parser.parse_args()
 
@@ -63,24 +79,28 @@ def temp_cd():
 python_replacement_string = f"python {args.python}*"
 
 try:
-    for dep_index, dep_value in enumerate(yaml_script['dependencies']):
-        if re.match('python([ ><=*]+[0-9.*]*)?$', dep_value):  # Match explicitly 'python' and its formats
-            yaml_script['dependencies'].pop(dep_index)
+    for dep_index, dep_value in enumerate(yaml_script["dependencies"]):
+        if re.match(
+            "python([ ><=*]+[0-9.*]*)?$", dep_value
+        ):  # Match explicitly 'python' and its formats
+            yaml_script["dependencies"].pop(dep_index)
             break  # Making the assumption there is only one Python entry, also avoids need to enumerate in reverse
 except (KeyError, TypeError):
     # Case of no dependencies key, or dependencies: None
-    yaml_script['dependencies'] = []
+    yaml_script["dependencies"] = []
 finally:
     # Ensure the python version is added in. Even if the code does not need it, we assume the env does
-    yaml_script['dependencies'].insert(0, python_replacement_string)
+    yaml_script["dependencies"].insert(0, python_replacement_string)
 
 # Figure out conda path
 if "CONDA_EXE" in os.environ:
     conda_path = os.environ["CONDA_EXE"]
 else:
     conda_path = shutil.which("conda")
 if conda_path is None:
-    raise RuntimeError("Could not find a conda binary in CONDA_EXE variable or in executable search path")
+    raise RuntimeError(
+        "Could not find a conda binary in CONDA_EXE variable or in executable search path"
+    )
 
 print(f"CONDA ENV NAME  {args.name}")
 print(f"PYTHON VERSION  {args.python}")
@@ -90,6 +110,6 @@ def temp_cd():
 # Write to a temp directory which will always be cleaned up
 with temp_cd():
     temp_file_name = "temp_script.yaml"
-    with open(temp_file_name, 'w') as f:
+    with open(temp_file_name, "w") as f:
         f.write(yaml.dump(yaml_script))
     sp.call(f"{conda_path} env create -n {args.name} -f {temp_file_name}", shell=True)

docs/conf.py

@@ -14,22 +14,25 @@
 # Incase the project was not installed
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
+
+sys.path.insert(0, os.path.abspath(".."))
 
 import missense_kinase_toolkit
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'missense-kinase-toolkit'
-copyright = ("2024, Jess White. Project structure based on the "
-             "Computational Molecular Science Python Cookiecutter version 1.1")
-author = 'Jess White'
+project = "missense-kinase-toolkit"
+copyright = (
+    "2024, Jess White. Project structure based on the "
+    "Computational Molecular Science Python Cookiecutter version 1.1"
+)
+author = "Jess White"
 
 # The short X.Y version
-version = ''
+version = ""
 # The full version, including alpha/beta/rc tags
-release = ''
+release = ""
 
 
 # -- General configuration ---------------------------------------------------
@@ -42,13 +45,13 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autosummary',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.extlinks',
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.extlinks",
 ]
 
 autosummary_generate = True
@@ -57,16 +60,16 @@
 napoleon_use_ivar = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -78,18 +81,18 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path .
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'default'
+pygments_style = "default"
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -100,7 +103,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -116,7 +119,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'missense_kinase_toolkitdoc'
+htmlhelp_basename = "missense_kinase_toolkitdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -125,15 +128,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -143,8 +143,13 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'missense_kinase_toolkit.tex', 'missense-kinase-toolkit Documentation',
-     'missense_kinase_toolkit', 'manual'),
+    (
+        master_doc,
+        "missense_kinase_toolkit.tex",
+        "missense-kinase-toolkit Documentation",
+        "missense_kinase_toolkit",
+        "manual",
+    ),
 ]
 
 
@@ -153,8 +158,13 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'missense_kinase_toolkit', 'missense-kinase-toolkit Documentation',
-     [author], 1)
+    (
+        master_doc,
+        "missense_kinase_toolkit",
+        "missense-kinase-toolkit Documentation",
+        [author],
+        1,
+    )
 ]
 
 
@@ -164,9 +174,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'missense_kinase_toolkit', 'missense-kinase-toolkit Documentation',
-     author, 'missense_kinase_toolkit', 'An ETL pipeline package to facilitate structure-based ML for human kinase property prediction',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "missense_kinase_toolkit",
+        "missense-kinase-toolkit Documentation",
+        author,
+        "missense_kinase_toolkit",
+        "An ETL pipeline package to facilitate structure-based ML for human kinase property prediction",
+        "Miscellaneous",
+    ),
 ]