Merge pull request #21 from ajshajib/formatting

Code formatting with black and docformatter

.github/workflows/ci_test.yml

@@ -26,7 +26,8 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install --upgrade pytest
-          python -m pip install flake8 pytest pytest-cov coveralls
+          python -m pip install flake8 pytest pytest-cov
+          python -m pip install codecov
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
           if [ -f test_requirements.txt ]; then pip install -r test_requirements.txt; fi
           python -m pip install .
@@ -36,15 +37,23 @@ jobs:
       #    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=127 --statistics
-      - name: Test with pytest
-        run: |
-          pytest --cov=hierarc
+      -   name: Test with pytest
+          run: |
+              pytest --cov=./ --cov-report=xml
+              codecov
 
-      - name: Coveralls
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          coveralls --service=github
+      -   name: Upload coverage reports to Codecov
+          uses: codecov/codecov-action@v3
+          env:
+              CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          with:
+              files: ./coverage.xml
+
+#      - name: Coveralls
+#        env:
+#          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#        run: |
+#          coveralls --service=github
 
       # from this source for coveralls: https://github.com/marketplace/actions/coveralls-github-action
       #- uses: actions/checkout@v1

.gitignore

@@ -102,4 +102,5 @@ ENV/
 .mypy_cache/
 
 # IDE settings
-.vscode/
+.vscode/
+.idea/

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+ci:
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit.com hooks
+    autofix_prs: true
+    autoupdate_branch: ''
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: monthly
+    skip: []
+    submodules: false
+
+repos:
+  - repo: https://github.com/psf/black
+    rev: 23.11.0
+    hooks:
+      - id: black
+        # It is recommended to specify the latest version of Python
+        # supported by your project here, or alternatively use
+        # pre-commit's default_language_version, see
+        # https://pre-commit.com/#top_level-default_language_version
+        language_version: python3
+  - repo: https://github.com/psf/black
+    rev: 23.11.0
+    hooks:
+      - id: black-jupyter
+        language_version: python3
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.5
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [-r, --black, --in-place]
+

Makefile

@@ -49,6 +49,8 @@ clean-test: ## remove test and coverage artifacts
 
 lint: ## check style with flake8
 	flake8 hierarc tests
+	black .
+	docformatter -r ./* --black --in-place
 
 test: ## run tests quickly with the default Python
 	pytest

README.rst

@@ -20,6 +20,15 @@ hierArc
         :target: http://www.astropy.org
         :alt: Powered by Astropy Badge
 
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+    :target: https://github.com/psf/black
+
+.. image:: https://img.shields.io/badge/%20formatter-docformatter-fedcba.svg
+    :target: https://github.com/PyCQA/docformatter
+
+.. image:: https://img.shields.io/badge/%20style-sphinx-0a507a.svg
+    :target: https://www.sphinx-doc.org/en/master/usage/index.html
+
 
 
 Hierarchical analysis of strong lensing systems to infer lens properties and cosmological parameters simultaneously.

codecov.yml

@@ -0,0 +1,6 @@
+comment:                  # this is a top-level key
+  layout: " diff, flags, files"
+  behavior: default
+  require_changes: false  # if true: only post the comment if coverage changes
+  require_base: false        # [true :: must have a base report to post]
+  require_head: true       # [true :: must have a head report to post]

docs/conf.py

@@ -19,7 +19,8 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
+
+sys.path.insert(0, os.path.abspath(".."))
 
 import hierarc
 
@@ -31,22 +32,22 @@
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode"]
 
 # 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"
 
 # General information about the project.
-project = 'hierArc'
+project = "hierArc"
 copyright = "2020, Simon Birrer"
 author = "Simon Birrer"
 
@@ -64,15 +65,15 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'en'
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to 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 = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -83,7 +84,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'default'
+html_theme = "default"
 
 # 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
@@ -94,13 +95,13 @@
 # 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"]
 
 
 # -- Options for HTMLHelp output ---------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'hierarcdoc'
+htmlhelp_basename = "hierarcdoc"
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -109,15 +110,12 @@
     # 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',
@@ -127,21 +125,15 @@
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'hierarc.tex',
-     'hierArc Documentation',
-     'Simon Birrer', 'manual'),
+    (master_doc, "hierarc.tex", "hierArc Documentation", "Simon Birrer", "manual"),
 ]
 
 
 # -- Options for manual page output ------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'hierarc',
-     'hierArc Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "hierarc", "hierArc Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------
@@ -150,13 +142,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'hierarc',
-     'hierArc Documentation',
-     author,
-     'hierarc',
-     'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "hierarc",
+        "hierArc Documentation",
+        author,
+        "hierarc",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
-
-
-

hierarc/Diagnostics/blinding.py

@@ -3,8 +3,7 @@
 
 
 def blind_posterior(posterior, param_names):
-    """
-    blinds H0 and lambda_int to default values
+    """Blinds H0 and lambda_int to default values.
 
     :param posterior: posterior samples of hierArc
     :type posterior: flattened posterior with num_param x num_samples array
@@ -14,10 +13,10 @@ def blind_posterior(posterior, param_names):
     """
     posterior_blind = copy.deepcopy(posterior)
     for i, param_name in enumerate(param_names):
-        if param_name == 'lambda_mst':
+        if param_name == "lambda_mst":
             # shift all lambda_int posteriors to a median = 1
             posterior_blind[:, i] *= 1 / np.median(posterior_blind[:, i])
-        if param_name == 'h0':
+        if param_name == "h0":
             # shift all H0 posteriors to a mean = 70
             posterior_blind[:, i] *= 70 / np.median(posterior_blind[:, i])
     return posterior_blind