Merge branch 'release/3.2.2'

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## [3.2.1](https://github.com/dermatologist/fhiry/tree/3.2.1) (2023-11-27)
+
+[Full Changelog](https://github.com/dermatologist/fhiry/compare/3.2.0...3.2.1)
+
 ## [3.2.0](https://github.com/dermatologist/fhiry/tree/3.2.0) (2023-11-20)
 
 [Full Changelog](https://github.com/dermatologist/fhiry/compare/3.1.0...3.2.0)

dev-requirements.in

@@ -5,6 +5,7 @@ pytest
 responses
 recommonmark
 sphinx>=3.2.1
+myst-parser[linkify]
 setuptools
 setuptools_scm
 wheel

dev-requirements.txt

@@ -30,13 +30,14 @@ distlib==0.3.2
     # via virtualenv
 docutils==0.17.1
     # via
+    #   myst-parser
     #   recommonmark
     #   sphinx
 filelock==3.0.12
     # via
     #   tox
     #   virtualenv
-idna==3.4
+idna==3.6
     # via
     #   -c requirements.txt
     #   requests
@@ -45,9 +46,23 @@ imagesize==1.2.0
 iniconfig==1.1.1
     # via pytest
 jinja2==3.0.1
-    # via sphinx
+    # via
+    #   myst-parser
+    #   sphinx
+linkify-it-py==1.0.3
+    # via myst-parser
+markdown-it-py==2.2.0
+    # via
+    #   mdit-py-plugins
+    #   myst-parser
 markupsafe==2.0.1
     # via jinja2
+mdit-py-plugins==0.3.5
+    # via myst-parser
+mdurl==0.1.2
+    # via markdown-it-py
+myst-parser[linkify]==0.18.1
+    # via -r dev-requirements.in
 packaging==23.2
     # via
     #   -c requirements.txt
@@ -77,6 +92,8 @@ pytz==2023.3.post1
     # via
     #   -c requirements.txt
     #   babel
+pyyaml==6.0.1
+    # via myst-parser
 recommonmark==0.7.1
     # via -r dev-requirements.in
 requests==2.31.0
@@ -98,6 +115,7 @@ snowballstemmer==2.1.0
 sphinx==4.4.0
     # via
     #   -r dev-requirements.in
+    #   myst-parser
     #   recommonmark
 sphinxcontrib-applehelp==1.0.2
     # via sphinx
@@ -124,6 +142,10 @@ tox==3.25.0
     # via -r dev-requirements.in
 types-toml==0.10.8.1
     # via responses
+typing-extensions==4.8.0
+    # via myst-parser
+uc-micro-py==1.0.2
+    # via linkify-it-py
 urllib3==2.1.0
     # via
     #   -c requirements.txt

docs/Makefile

@@ -11,7 +11,7 @@ AUTODOCDIR    = api
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $?), 1)
-$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/")
+$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from https://sphinx-doc.org/")
 endif
 
 .PHONY: help clean Makefile

docs/conf.py

@@ -9,14 +9,11 @@
 
 import os
 import sys
-import inspect
 import shutil
 
 # -- Path setup --------------------------------------------------------------
 
-__location__ = os.path.join(
-    os.getcwd(), os.path.dirname(inspect.getfile(inspect.currentframe()))
-)
+__location__ = os.path.dirname(__file__)
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -26,7 +23,7 @@
 # -- Run sphinx-apidoc -------------------------------------------------------
 # This hack is necessary since RTD does not issue `sphinx-apidoc` before running
 # `sphinx-build -b html . _build/html`. See Issue:
-# https://github.com/rtfd/readthedocs.org/issues/1139
+# https://github.com/readthedocs/readthedocs.org/issues/1139
 # DON'T FORGET: Check the box "Install your project inside a virtualenv using
 # setup.py install" in the RTD Advanced Settings.
 # Additionally it helps us to avoid running apidoc manually
@@ -46,10 +43,7 @@
 try:
     import sphinx
 
-    cmd_line_template = (
-        "sphinx-apidoc --implicit-namespaces -f -o {outputdir} {moduledir}"
-    )
-    cmd_line = cmd_line_template.format(outputdir=output_dir, moduledir=module_dir)
+    cmd_line = f"sphinx-apidoc --implicit-namespaces -f -o {output_dir} {module_dir}"
 
     args = cmd_line.split(" ")
     if tuple(sphinx.__version__.split(".")) >= ("1", "7"):
@@ -84,25 +78,22 @@
 templates_path = ["_templates"]
 
 
-# Configure AutoStructify
-# https://recommonmark.readthedocs.io/en/latest/auto_structify.html
-def setup(app):
-    from recommonmark.transform import AutoStructify
-
-    params = {
-        "enable_auto_toc_tree": True,
-        "auto_toc_tree_section": "Contents",
-        "auto_toc_maxdepth": 2,
-        "enable_eval_rst": True,
-        "enable_math": True,
-        "enable_inline_math": True,
-    }
-    app.add_config_value("recommonmark_config", params, True)
-    app.add_transform(AutoStructify)
-
-
 # Enable markdown
-extensions.append("recommonmark")
+extensions.append("myst_parser")
+
+# Configure MyST-Parser
+myst_enable_extensions = [
+    "amsmath",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "html_image",
+    "linkify",
+    "replacements",
+    "smartquotes",
+    "substitution",
+    "tasklist",
+]
 
 # The suffix of source filenames.
 source_suffix = [".rst", ".md"]
@@ -115,16 +106,25 @@ def setup(app):
 
 # General information about the project.
 project = "fhiry"
-copyright = "2021, Bell Eapen"
+copyright = "2023, Bell Eapen"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-# The short X.Y version.
-version = ""  # Is set by calling `setup.py docs`
-# The full version, including alpha/beta/rc tags.
-release = ""  # Is set by calling `setup.py docs`
+# version: The short X.Y version.
+# release: The full version, including alpha/beta/rc tags.
+# If you don’t need the separation provided between version and release,
+# just set them both to the same value.
+try:
+    from fhiry import __version__ as version
+except ImportError:
+    version = ""
+
+if not version or version.lower() == "unknown":
+    version = os.getenv("READTHEDOCS_VERSION", "unknown")  # automatically set by RTD
+
+release = version
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -163,6 +163,9 @@ def setup(app):
 # If true, keep warnings as "system message" paragraphs in the built documents.
 # keep_warnings = False
 
+# If this is True, todo emits a warning for each TODO entries. The default is False.
+todo_emit_warnings = True
+
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -183,12 +186,7 @@ def setup(app):
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-try:
-    from src.fhiry import __version__ as version
-except ImportError:
-    pass
-else:
-    release = version
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 # html_short_title = None
@@ -292,12 +290,15 @@ def setup(app):
 # -- External mapping --------------------------------------------------------
 python_version = ".".join(map(str, sys.version_info[0:2]))
 intersphinx_mapping = {
-    "sphinx": ("http://www.sphinx-doc.org/en/stable", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master", None),
     "python": ("https://docs.python.org/" + python_version, None),
     "matplotlib": ("https://matplotlib.org", None),
-    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
     "sklearn": ("https://scikit-learn.org/stable", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "setuptools": ("https://setuptools.pypa.io/en/stable/", None),
     "pyscaffold": ("https://pyscaffold.org/en/stable", None),
 }
+
+print(f"loading configurations for {project} {version} ...", file=sys.stderr)

docs/index.md

@@ -2,6 +2,8 @@
 
 FHIR to pandas.dataframe for AI and ML
 
+[by Bell Eapen](https://nuchange.ca)
+
 
 ## Contents
 
@@ -14,18 +16,15 @@ Contributions & Help <contributing>
 License <license>
 Authors <authors>
 Changelog <changelog>
-
+```
 
 ## Indices and tables
 
-```eval_rst
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-```
+* {ref}`genindex`
+* {ref}`modindex`
+* {ref}`search`
 
 [Sphinx]: http://www.sphinx-doc.org/
 [Markdown]: https://daringfireball.net/projects/markdown/
 [reStructuredText]: http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
-[recommonmark]: https://recommonmark.readthedocs.io/en/latest
-[autostructify]: https://recommonmark.readthedocs.io/en/latest/auto_structify.html
+[MyST]: https://myst-parser.readthedocs.io/en/latest/

docs/requirements.txt

@@ -4,3 +4,4 @@
 # sphinx_rtd_theme
 recommonmark
 sphinx>=3.2.1
+myst-parser[linkify]

requirements.txt

@@ -40,7 +40,7 @@ grpcio==1.59.3
     #   grpcio-status
 grpcio-status==1.59.3
     # via google-api-core
-idna==3.4
+idna==3.6
     # via requests
 numpy==1.26.2
     # via
@@ -66,7 +66,7 @@ protobuf==4.25.1
     #   proto-plus
 pyarrow==14.0.1
     # via db-dtypes
-pyasn1==0.5.0
+pyasn1==0.5.1
     # via
     #   pyasn1-modules
     #   rsa

setup.cfg

@@ -129,7 +129,7 @@ exclude =
 [pyscaffold]
 # PyScaffold's parameters when the project was created.
 # This will be used when updating. Do not change!
-version = 4.0.2
+version = 4.5
 package = fhiry
 extensions =
     markdown

setup.py

@@ -2,7 +2,7 @@
     Setup file for fhiry.
     Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.0.2.
+    This file was generated with PyScaffold 4.5.
     PyScaffold helps you to put up the scaffold of your new Python project.
     Learn more under: https://pyscaffold.org/
 """

update.sh

@@ -0,0 +1,2 @@
+pip-compile --upgrade
+pip-compile dev-requirements.in