Move package metadata and tool configuration to pyproject.toml

.gitignore

@@ -119,3 +119,6 @@ tlo.conf
 # ignore all files in outputs directory, except README
 outputs/*
 !outputs/README
+
+# ignore _version.py file generated by setuptools_scm
+src/**/_version.py

MANIFEST.in

@@ -4,8 +4,6 @@ graft tests
 graft requirements
 
 include README.rst
-include .bumpversion.cfg
-include .coveragerc
 include tox.ini
 include tlo.example.conf
 include CITATION.cff

docs/conf.py

@@ -9,6 +9,7 @@
 
 import os
 import sys
+from importlib.metadata import version as get_version
 
 sys.path.insert(0, os.path.abspath('../..')), os.path.abspath('../src')
 
@@ -39,7 +40,8 @@
 year = '2021'
 author = 'The TLOmodel Team'
 copyright = '{0}, {1}'.format(year, author)
-version = release = '0.1.0'
+release = get_version('setuptools_scm')
+version = ".".join(release.split('.')[:2])
 
 pygments_style = 'trac'
 templates_path = ['.']

pyproject.toml

@@ -0,0 +1,144 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = ["setuptools>=62", "setuptools_scm[toml]>=8.0"]
+
+[project]
+name = "tlo"
+authors = [
+    {name = "Thanzi La Onse Model Development Team"},
+]
+classifiers = [
+    'Development Status :: 3 - Alpha',
+    'Intended Audience :: Science/Research',
+    'License :: MIT',
+    'Operating System :: OS Independent',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3 :: Only',
+    'Programming Language :: Python :: 3.8',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
+]
+dependencies = [
+    "GitPython",
+    "click",
+    "matplotlib",
+    "pyshp",
+    "squarify",
+    "numpy",
+    "pandas~=2.0.0",
+    "scipy",
+     # Avoid https://foss.heptapod.net/openpyxl/openpyxl/-/issues/1963
+    "openpyxl==3.1.0",
+    # To submit jobs to Azure Batch
+    "azure-batch",
+    "azure-identity",
+    "azure-keyvault",
+    "azure-storage-file-share",
+]
+description = "Thanzi la Onse Epidemiology Model"
+dynamic = ["version"]
+license = {file = "LICENSE.txt"}
+readme = "README.rst"
+requires-python = ">=3.8"
+
+[project.optional-dependencies]
+dev = [
+    # Running tests
+    "pytest",
+    "pytest-cov",
+    "pytest-xdist",
+    "virtualenv",
+    "tox",
+    # Linting
+    "isort",
+    "pylint",
+    "ruff",
+    # Profiling
+    "pyinstrument>=4.3",
+    # Building requirements files
+    "pip-tools",
+]
+
+[project.scripts]
+tlo = "tlo.cli:cli"
+
+[project.urls]
+repository = "https://github.com/UCL/TLOmodel"
+documentation = "https://tlomodel.org"
+
+[tool.coverage]
+report = {show_missing = true, precision = 2}
+run = {branch = true, parallel = true, source = [
+    "tlo",
+    "tests"
+]}
+paths.source = [
+    "src",
+    "*/site-packages",
+]
+
+[tool.isort]
+force_single_line = false
+multi_line_output = 3
+include_trailing_comma = true
+line_length = 100
+known_first_party = "tlo"
+default_section = "THIRDPARTY"
+
+[tool.pylint.main]
+extension-pkg-whitelist = ["numpy"]
+disable = [
+    "R",
+    "C",
+    "W",
+    "E0110", # abstract class instantiated
+    "E0611", # no-name-in-module
+    "E0702", # raising NoneType
+    "E1136", # unsubscriptable type
+    "E1137", # doesn't support item assignment
+    "E1101", # no-member
+    "E1120", # no-value-for-parameter
+    "E1130", # bad operand type for unary ~
+]
+
+
+[tool.pylint.typecheck]
+signature-mutators = [
+    "click.decorators.option",
+    "click.decorators.argument",
+    "click.decorators.version_option",
+    "click.decorators.help_option",
+    "click.decorators.pass_context",
+    "click.decorators.confirmation_option",
+]
+
+[tool.pytest.ini_options]
+testpaths = "tests"
+python_files = [
+    "test_*.py",
+    "*_test.py",
+    "tests.py",
+]
+addopts = "-ra --strict-markers --doctest-modules --doctest-glob=*.rst --tb=short"
+markers = ["group2", "slow"]
+
+[tool.ruff]
+target-version = "py38"
+line-length = 120
+ignore = [
+    "E712", # comparison to False
+    "E713", # use `not in`
+    "E714", # use `is not`
+    "E721", # do not compare types
+    "E731", # do not assign a lambda expression
+    "E741", # ambiguous variable name
+    "F601", # dictionary literal key repeated
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools_scm]
+version_file  = "src/tlo/_version.py"

requirements/base.txt

@@ -1,13 +1,13 @@
 #
-# This file is autogenerated by pip-compile
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
 #
-#    pip-compile --output-file=base.txt base.in
+#    pip-compile --output-file=/home/matt/projects/TLOmodel/requirements/base.txt
 #
 adal==1.2.7
     # via msrestazure
 azure-batch==14.0.0
-    # via -r base.in
+    # via tlo (pyproject.toml)
 azure-common==1.1.28
     # via
     #   azure-batch
@@ -23,17 +23,17 @@ azure-core==1.29.4
     #   azure-storage-file-share
     #   msrest
 azure-identity==1.14.0
-    # via -r base.in
+    # via tlo (pyproject.toml)
+azure-keyvault==4.2.0
+    # via tlo (pyproject.toml)
 azure-keyvault-certificates==4.7.0
     # via azure-keyvault
 azure-keyvault-keys==4.8.0
     # via azure-keyvault
 azure-keyvault-secrets==4.7.0
     # via azure-keyvault
-azure-keyvault==4.2.0
-    # via -r base.in
 azure-storage-file-share==12.14.1
-    # via -r base.in
+    # via tlo (pyproject.toml)
 certifi==2023.7.22
     # via
     #   msrest
@@ -43,7 +43,7 @@ cffi==1.15.1
 charset-normalizer==3.2.0
     # via requests
 click==8.1.7
-    # via -r base.in
+    # via tlo (pyproject.toml)
 contourpy==1.1.1
     # via matplotlib
 cryptography==41.0.3
@@ -63,11 +63,9 @@ fonttools==4.42.1
 gitdb==4.0.10
     # via gitpython
 gitpython==3.1.36
-    # via -r base.in
+    # via tlo (pyproject.toml)
 idna==3.4
     # via requests
-importlib-resources==6.0.1
-    # via matplotlib
 isodate==0.6.1
     # via
     #   azure-keyvault-certificates
@@ -78,32 +76,32 @@ isodate==0.6.1
 kiwisolver==1.4.5
     # via matplotlib
 matplotlib==3.7.3
-    # via -r base.in
-msal-extensions==1.0.0
-    # via azure-identity
+    # via tlo (pyproject.toml)
 msal==1.24.0
     # via
     #   azure-identity
     #   msal-extensions
+msal-extensions==1.0.0
+    # via azure-identity
 msrest==0.7.1
     # via msrestazure
 msrestazure==0.6.4
     # via azure-batch
 numpy==1.24.4
     # via
-    #   -r base.in
     #   contourpy
     #   matplotlib
     #   pandas
     #   scipy
+    #   tlo (pyproject.toml)
 oauthlib==3.2.2
     # via requests-oauthlib
 openpyxl==3.1.0
-    # via -r base.in
+    # via tlo (pyproject.toml)
 packaging==23.1
     # via matplotlib
 pandas==2.0.3
-    # via -r base.in
+    # via tlo (pyproject.toml)
 pillow==10.0.1
     # via matplotlib
 portalocker==2.8.2
@@ -117,25 +115,25 @@ pyjwt[crypto]==2.8.0
 pyparsing==3.1.1
     # via matplotlib
 pyshp==2.3.1
-    # via -r base.in
+    # via tlo (pyproject.toml)
 python-dateutil==2.8.2
     # via
     #   adal
     #   matplotlib
     #   pandas
 pytz==2023.3.post1
     # via pandas
-requests-oauthlib==1.3.1
-    # via msrest
 requests==2.31.0
     # via
     #   adal
     #   azure-core
     #   msal
     #   msrest
     #   requests-oauthlib
+requests-oauthlib==1.3.1
+    # via msrest
 scipy==1.10.1
-    # via -r base.in
+    # via tlo (pyproject.toml)
 six==1.16.0
     # via
     #   azure-core
@@ -145,7 +143,7 @@ six==1.16.0
 smmap==5.0.1
     # via gitdb
 squarify==0.4.3
-    # via -r base.in
+    # via tlo (pyproject.toml)
 typing-extensions==4.8.0
     # via
     #   azure-core
@@ -157,5 +155,3 @@ tzdata==2023.3
     # via pandas
 urllib3==2.0.4
     # via requests
-zipp==3.16.2
-    # via importlib-resources