Replace versioneer with setuptools_scm. (#111)

.gitignore

@@ -150,3 +150,4 @@ docs/source/tutorials/.sid_*
 # sid
 .sid/
 src/__init__.py
+src/sid/_version.py

.pre-commit-config.yaml

@@ -1,23 +1,22 @@
 repos:
--   repo: https://github.com/econchick/interrogate
-    rev: 1.3.2
-    hooks:
-    -   id: interrogate
-        args: [
-            -v,
-            --fail-under=78,
-            --generate-badge=docs/source/_static/images/interrogate_badge.svg,
-            src,
-        ]
-        pass_filenames: false
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v3.4.0
     hooks:
+    -   id: check-added-large-files
+        args: ['--maxkb=500']
+    -   id: check-case-conflict
     -   id: check-merge-conflict
+    -   id: check-vcs-permalinks
+    -   id: check-yaml
+        exclude: meta.yaml
     -   id: debug-statements
     -   id: end-of-file-fixer
-    -   id: check-added-large-files
-        args: ['--maxkb=500']
+    -   id: fix-byte-order-marker
+    -   id: forbid-new-submodules
+    -   id: mixed-line-ending
+    -   id: no-commit-to-branch
+        args: [--branch, main]
+    -   id: trailing-whitespace
 -   repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.8.0  # Use the ref you want to point at
     hooks:
@@ -32,7 +31,7 @@ repos:
     -   id: rst-inline-touching-normal
     -   id: text-unicode-replacement-char
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.12.0
+    rev: v2.13.0
     hooks:
     -   id: pyupgrade
         args: [--py36-plus]
@@ -41,6 +40,10 @@ repos:
     hooks:
     -   id: reorder-python-imports
         types: [python]
+-   repo: https://github.com/asottile/setup-cfg-fmt
+    rev: v1.17.0
+    hooks:
+    -   id: setup-cfg-fmt
 -   repo: https://github.com/psf/black
     rev: 20.8b1
     hooks:
@@ -81,6 +84,12 @@ repos:
     rev: 0.9.0a1
     hooks:
     -   id: doc8
+-   repo: https://github.com/econchick/interrogate
+    rev: 1.3.2
+    hooks:
+    -   id: interrogate
+        args: [-v, --fail-under=78, src]
+        pass_filenames: false
 -   repo: https://github.com/codespell-project/codespell
     rev: v2.0.0
     hooks:

MANIFEST.in

@@ -1,7 +1,5 @@
 include CITATION
 include LICENSE
-include versioneer.py
-include src/sid/_version.py
 
 recursive-include src *.csv
 

README.rst

@@ -37,9 +37,6 @@ sid
 .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
     :target: https://github.com/psf/black
 
-.. image:: https://sid-dev.readthedocs.io/en/latest/_static/images/interrogate_badge.svg
-    :target: https://github.com/econchick/interrogate
-
 .. end-badges
 
 

codecov.yml

@@ -25,5 +25,3 @@ coverage:
 ignore:
   - ".tox/**/*"
   - "setup.py"
-  - "versioneer.py"
-  - "src/sid/_version.py"

docs/rtd_environment.yml

@@ -4,6 +4,9 @@ channels:
 
 dependencies:
   - python >= 3.6
+  - pip
+  - setuptools_scm
+  - toml
 
   # Sphinx dependencies.
   - furo
@@ -24,3 +27,6 @@ dependencies:
   - python-snappy
   - seaborn
   - tqdm
+
+  - pip:
+    - ../

docs/source/changes.rst

@@ -7,7 +7,7 @@ all releases are available on `Anaconda.org
 <https://anaconda.org/covid-19-impact-lab/sid>`_.
 
 
-0.0.4 - 2021-xx-xx
+0.0.4 - 2021-04-24
 ------------------
 
 - :gh:`92` adds an interface for rapid tests.
@@ -26,6 +26,8 @@ all releases are available on `Anaconda.org
 - :gh:`107` allows compute derived state variables which can be used across model
   features to save some computations.
 - :gh:`108` enhances dtype conversion of random contact models.
+- :gh:`110` fixes a ``SettingWithCopy`` warning in ``contacts.py``.
+- :gh:`111` leads the migration from ``versioneer`` to ``setuptools_scm``.
 
 
 0.0.3 - 2021-03-23

docs/source/conf.py

@@ -1,30 +1,23 @@
-# Configuration file for the Sphinx documentation builder.
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
+# Configuration file for the Sphinx documentation builder. This file only contains a
+# selection of the most common options. For a full list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
-# -- Path setup --------------------------------------------------------------
-# 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.
-import os
-import sys
-from datetime import datetime
+import datetime as dt
 
-
-sys.path.insert(0, os.path.abspath("../../src"))
-
-
-import sid  # noqa: E402
+from pkg_resources import get_distribution
 
 
 # -- Project information -----------------------------------------------------
 
 project = "sid"
-year = datetime.now().year
+year = dt.datetime.now().year
 copyright = f"2020-{year}, Janos Gabler, Tobias Raabe, Klara Röhrl"  # noqa: A001
 author = "Janos Gabler, Tobias Raabe, Klara Röhrl"
-version = sid.__version__
-release = version
+
+# The version, including alpha/beta/rc tags, but not commit hash and datestamps
+release = get_distribution("sid-dev").version.split("+")[0]
+# The short X.Y version.
+version = release
+
 
 # -- General configuration ---------------------------------------------------
 
@@ -146,7 +139,7 @@
 html_show_copyright = True
 
 html_theme_options = {
-    "sidebar_hide_name": True,
+    "sidebar_hide_name": False,
     "navigation_with_keys": True,
 }
 

docs/source/index.rst

@@ -11,7 +11,7 @@ sid
    :end-before: end-installation
 
 More information can be found in the `discussion paper <https://www.iza.org/
-publications/ dp/13899>`_ or in the four following chapters of the documentation.
+publications/dp/13899>`_ or in the four following chapters of the documentation.
 
 
 Documentation

environment.yml

@@ -8,6 +8,8 @@ channels:
 dependencies:
   - python >=3.6
   - pip
+  - setuptools_scm
+  - toml
 
   # Conda
   - anaconda-client

pyproject.toml

@@ -1,3 +1,9 @@
+[build-system]
+requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.0"]
+
+[tool.setuptools_scm]
+write_to = "src/sid/_version.py"
+
 [tool.nbqa.config]
 isort = "setup.cfg"
 black = "pyproject.toml"

setup.cfg

@@ -1,10 +1,53 @@
-# See the docstring in versioneer.py for instructions. Note that you must re-run
-# 'versioneer.py setup' after changing this section, and commit the resulting files.
+[metadata]
+name = sid_dev
+description = Simulate the spread of COVID-19 with different policies.
+long_description = file: README.rst
+long_description_content_type = text/x-rst
+url = https://github.com/covid-19-impact-lab/sid
+author = Janos Gabler, Tobias Raabe, Klara Roehrl
+author_email = [email protected]
+license = MIT
+license_file = LICENSE
+platforms = any
+classifiers =
+    Development Status :: 3 - Alpha
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Topic :: Scientific/Engineering
+project_urls =
+    Changelog = https://sid-dev.readthedocs.io/en/latest/changes.html
+    Documentation = https://sid-dev.readthedocs.io/en/latest
+    Github = https://github.com/covid-19-impact-lab/sid
+    Tracker = https://github.com/covid-19-impact-lab/sid/issues
 
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = src/sid/_version.py
-versionfile_build = sid/_version.py
-tag_prefix = v
-parentdir_prefix = sid-
+[options]
+packages = find:
+install_requires =
+    bokeh
+    dask
+    fastparquet
+    numba>=0.48
+    numpy
+    pandas>=1
+    python-snappy
+    seaborn
+    tqdm
+python_requires = >=3.6
+include_package_data = True
+package_dir =
+    =src
+zip_safe = False
+
+[options.packages.find]
+where = src
+
+[check-manifest]
+ignore =
+    src/sid/_version.py