Transition to pyproject.toml

.git-blame-ignore-revs

@@ -1,3 +1,5 @@
 # .git-blame-ignore-revs
 # apply isort, black and docformatter to code base
-6a9346b581883b4f29982c8ef1102a4b1a102664
+6a9346b581883b4f29982c8ef1102a4b1a102664
+# apply isort, black, docformatter to submodules in pastas
+9f58ed52e0151a525e7ad67e14bfd9217f4aa773

.github/workflows/ci.yml

@@ -36,13 +36,12 @@ jobs:
           pip install codacy-coverage
           pip install -e .
 
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=80 --statistics
-
+      - name: Lint with black
+        uses: psf/black@stable
+        with:
+          options: "--check --verbose"
+          jupyter: true
+
       - name: Run tests and notebooks
         if: ${{ github.event_name == 'pull_request' }}
         run: |

.readthedocs.yml

@@ -29,7 +29,9 @@ sphinx:
 python:
   system_packages: true
   install:
-    - requirements: requirements.rtd.txt
-    - requirements: requirements.ci.txt
     - method: pip
       path: .
+      extra_requirements:
+        - rtd
+        - ci
+

doc/conf.py

@@ -13,74 +13,72 @@
 # serve to show the default.
 
 import os
+import re
 import sys
 from datetime import date
 
 import requests
-import re
 
 year = date.today().strftime("%Y")
 
 from matplotlib import use
 
-use('agg')
-
-from pastas.version import __version__
+use("agg")
 
 from dataclasses import dataclass, field
-import sphinxcontrib.bibtex.plugin
 
+import sphinxcontrib.bibtex.plugin
 from sphinxcontrib.bibtex.style.referencing import BracketStyle
-from sphinxcontrib.bibtex.style.referencing.author_year \
-    import AuthorYearReferenceStyle
+from sphinxcontrib.bibtex.style.referencing.author_year import AuthorYearReferenceStyle
+
+from pastas.version import __version__
 
 # 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
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath("."))
 
 # -- General configuration ------------------------------------------------
 
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'IPython.sphinxext.ipython_console_highlighting',  # lowercase didn't work
-    'sphinx.ext.autosectionlabel',
-    'nbsphinx',
-    'sphinx_gallery.load_style',
-    'sphinxcontrib.bibtex',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "IPython.sphinxext.ipython_console_highlighting",  # lowercase didn't work
+    "sphinx.ext.autosectionlabel",
+    "nbsphinx",
+    "sphinx_gallery.load_style",
+    "sphinxcontrib.bibtex",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-source_suffix = '.rst'
-source_encoding = 'utf-8'
+templates_path = ["_templates"]
+source_suffix = ".rst"
+source_encoding = "utf-8"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'Pastas'
-copyright = u'{}, R.A. Collenteur, M. Bakker, R. Calje, F. Schaars'.format(
-    year)
-author = u'R.A. Collenteur, M. Bakker, R. Calje, F. Schaars'
+project = "Pastas"
+copyright = "{}, R.A. Collenteur, M. Bakker, R. Calje, F. Schaars".format(year)
+author = "R.A. Collenteur, M. Bakker, R. Calje, F. Schaars"
 
 # The version.
 version = __version__
 release = __version__
-language = 'en'
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build', '**.ipynb_checkpoints']
+exclude_patterns = ["_build", "**.ipynb_checkpoints"]
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -98,7 +96,7 @@
 show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -113,18 +111,18 @@
 
 html_theme = "pydata_sphinx_theme"
 html_logo = "_static/logo.png"
-html_static_path = ['_static']
+html_static_path = ["_static"]
 html_short_title = "Pastas"
 html_favicon = "_static/favo.ico"
-html_css_files = ['css/custom.css']
+html_css_files = ["css/custom.css"]
 html_show_sphinx = True
 html_show_copyright = True
-htmlhelp_basename = 'Pastasdoc'  # Output file base name for HTML help builder.
+htmlhelp_basename = "Pastasdoc"  # Output file base name for HTML help builder.
 html_use_smartypants = True
 
 html_theme_options = {
     "github_url": "https://github.com/pastas/pastas",
-    "use_edit_page_button": False
+    "use_edit_page_button": False,
 }
 
 html_context = {
@@ -145,7 +143,10 @@
 
 # support Round brackets
 def bracket_style() -> BracketStyle:
-    return BracketStyle(left='(', right=')', )
+    return BracketStyle(
+        left="(",
+        right=")",
+    )
 
 
 @dataclass
@@ -158,48 +159,41 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
 
 
 sphinxcontrib.bibtex.plugin.register_plugin(
-    'sphinxcontrib.bibtex.style.referencing',
-    'author_year_round', MyReferenceStyle)
+    "sphinxcontrib.bibtex.style.referencing", "author_year_round", MyReferenceStyle
+)
 
 # Generate bibliography-files from Zotero library
 # Get a Bibtex reference file from the Zotero group for referencing
 url = "https://api.zotero.org/groups/4846685/collections/8UG7PVLY/items/"
-params = {"format": "bibtex",
-          "style": "apa",
-          "limit": 100}
+params = {"format": "bibtex", "style": "apa", "limit": 100}
 
 r = requests.get(url=url, params=params)
 with open("references.bib", mode="w") as file:
     file.write(r.text)
 
 # Get a Bibtex reference file from the Zotero group for publications list
 url = "https://api.zotero.org/groups/4846685/collections/Q4F7R59G/items/"
-params = {"format": "bibtex",
-          "style": "apa",
-          "limit": 100}
+params = {"format": "bibtex", "style": "apa", "limit": 100}
 
 r = requests.get(url=url, params=params)
 with open("publications.bib", mode="w") as file:
     # Replace citation key to prevent duplicate labels and article now shown
-    text = re.sub(r'(@([a-z]*){)', r'\1X_', r.text)
+    text = re.sub(r"(@([a-z]*){)", r"\1X_", r.text)
     file.write(text)
 
 # Add some settings for bibtex
-bibtex_bibfiles = ['references.bib', 'publications.bib']
+bibtex_bibfiles = ["references.bib", "publications.bib"]
 bibtex_reference_style = "author_year_round"
 
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
     # 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',
 }
@@ -208,8 +202,13 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'Pastas.tex', u'Pastas Documentation',
-     u'R.A. Collenteur, M. Bakker, R. Calje, F. Schaars', 'manual'),
+    (
+        master_doc,
+        "Pastas.tex",
+        "Pastas Documentation",
+        "R.A. Collenteur, M. Bakker, R. Calje, F. Schaars",
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -237,10 +236,7 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'pastas', u'Pastas Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "pastas", "Pastas Documentation", [author], 1)]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -252,9 +248,15 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'Pastas', u'Pastas Documentation',
-     author, 'Pastas', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "Pastas",
+        "Pastas Documentation",
+        author,
+        "Pastas",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 # Example configuration for intersphinx: refer to the Python standard library.