Clean pre-commit And pyproject.toml (#54)

* minor update to pyproject toml; update precommit config file

* remove action yaml

* update labels

* update pyproject toml

* do not use R precommit hook for now

.github/workflows/pre-commit.yaml

@@ -9,6 +9,6 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
-    - uses: ./.github/actions/pre-commit
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+    - uses: pre-commit/[email protected]

.lintr

@@ -0,0 +1,2 @@
+linters: linters_with_defaults(object_usage_linter = NULL)
+encoding: "UTF-8"

.pre-commit-config.yaml

@@ -1,52 +1,147 @@
+################################################################################
+# OVERVIEW
+################################################################################
+# The following contains the pre-commit hooks for this repository, which are
+# likely a modified version of the author's (AFg6K7h4fhy2) repository template.
+#
+# Links:
+#
+# Pre-commit: https://pre-commit.com/
+# The author's template: https://github.com/AFg6K7h4fhy2/AFg6K7h4fhy2-Template
+# Supported hooks: https://github.com/pre-commit/pre-commit-hooks
 repos:
 ################################################################################
+# GENERAL
+################################################################################
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
+    # prevent giant files from being committed.
     -   id: check-added-large-files
         args: ["--maxkb=10000"]
+    # simply check whether files parse as valid
+    # python
+    -   id: check-ast
+    # check for files with names that would
+    # conflict on a case-insensitive filesystem
+    # like MacOS HFS+ or Windows FAT.
+    -   id: check-case-conflict
+    # checks for a common error of placing
+    # code before the docstring.
+    -   id: check-docstring-first
+    # attempts to load all yaml files to
+    # verify syntax.
     -   id: check-yaml
+        # allow yaml files which use the
+        # multi-document syntax
         args: ["--allow-multiple-documents"]
+    # attempts to load all TOML files to
+    # verify syntax.
     -   id: check-toml
+    # makes sure files end in a newline and
+    # only a newline.
     -   id: end-of-file-fixer
+    # replaces or checks mixed line ending.
     -   id: mixed-line-ending
+    # verifies that test files are named
+    # correctly.
+    -   id: name-tests-test
+        # ensure tests match test_.*\.py
+        args: ["--pytest-test-first"]
+    # checks that all your JSON files are pretty.
+    # "Pretty" here means that keys are sorted
+    # and indented.
+    -   id: pretty-format-json
+        # automatically format json files;
+        # when autofixing, retain the original
+        # key ordering (instead of sorting
+        # the keys)
+        args: ["--autofix", "--no-sort-keys"]
+    # trims trailing whitespace.
     -   id: trailing-whitespace
+    # checks that non-binary executables have
+    # a proper shebang.
+    -   id: check-executables-have-shebangs
+        files: \.sh$
+    # checks for the existence of private keys.
+    -   id: detect-private-key
+################################################################################
+# PYTHON
 ################################################################################
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
+    rev: 24.10.0
     hooks:
-    -   id: black-jupyter
+    -   id: black
         args: ["--line-length", "79"]
         language_version: python3
 -   repo: https://github.com/PyCQA/isort
     rev: 5.13.2
     hooks:
     -   id: isort
-        args: ["--profile", "black",
-               "--line-length", "79"]
--   repo: https://github.com/numpy/numpydoc
-    rev: v1.7.0
-    hooks:
-    -   id: numpydoc-validation
+        args: ["--profile", "black", "--line-length", "79"]
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.7
+    rev: v0.8.2
     hooks:
       - id: ruff
         args: ["--ignore=E741", "--ignore=E731", "--fix"]
+# -   repo: https://github.com/pre-commit/mirrors-mypy
+#     rev: v1.13.0
+#     hooks:
+#       - id: mypy
+################################################################################
+# R
+################################################################################
+# -   repo: https://github.com/lorenzwalthert/precommit
+#     rev: v0.4.3.9003
+#     hooks:
+#     -   id: style-files
+#     -   id: lintr
+################################################################################
+# MAKE FILES
+################################################################################
+-   repo: https://github.com/mrtazz/checkmake.git
+    rev: 0.2.2
+    hooks:
+    -   id: checkmake
+################################################################################
+# SECURITY
+################################################################################
+# -   repo: https://github.com/gitleaks/gitleaks
+#     rev: v8.19.0
+#     hooks:
+#     -   id: gitleaks
+# -   repo: https://github.com/Yelp/detect-secrets
+#     rev: v1.5.0
+#     hooks:
+#     # must first run
+#     # detect-secrets scan > .secrets.baseline
+#     -   id: detect-secrets
+#         args: ["--baseline", ".secrets.baseline"]
+#         exclude: package.lock.json
+################################################################################
+# GITHUB ACTIONS
 ################################################################################
 -   repo: https://github.com/rhysd/actionlint
-    rev: v1.7.1
+    rev: v1.7.4
     hooks:
     -   id: actionlint
 ################################################################################
+# SPELLING
+################################################################################
 -   repo: https://github.com/crate-ci/typos
-    rev: v1.21.0
+    rev: typos-dict-v0.11.37
     hooks:
     -   id: typos
         args: ["--force-exclude"]
 ################################################################################
+# COMMIT MESSAGES
+################################################################################
 -   repo: https://github.com/commitizen-tools/commitizen
-    rev: v3.27.0
+    rev: v4.0.0
     hooks:
     -   id: commitizen
+-   repo: https://github.com/jorisroovers/gitlint
+    rev:  v0.19.1
+    hooks:
+    -   id: gitlint
 ################################################################################

labels.toml

@@ -158,6 +158,11 @@ color = "cfd3d7"
 name = "visuals"
 description = "Adds or pertains to visualizations."
 
+[warnings]
+color = "cfd3d7"
+name = "warnings"
+description = "Adjustments to project to remove warnings."
+
 [website]
 color = "cfd3d7"
 name = "website"

pyproject.toml

@@ -1,10 +1,13 @@
 [tool.poetry]
 name = "genetic-evolution-tournament"
 version = "0.0.1"
-description = "The Genetic Evolution Tournament."
+description = "The Genetic Evolution Tournament (GET) is a Metaculus human judgment forecasting tournament established to generate forecasts and scenarios pertaining to the use of human genetic and reproductive technologies for treatment and enhancement."
 authors = ["AFg6K7h4fhy2 <[email protected]>"]
 license = "Apache-2.0"
 package-mode = false
+readme = "README.md"
+repository = "https://github.com/AFg6K7h4fhy2/Genetic-Evolution-Tournament"
+keywords = ["genetics", "tournament", "forecasting", "genetic-engineering", "human-enhancement", "human-judgment", "dna-technology"]
 
 [tool.poetry.dependencies]
 python = "^3.12"
@@ -14,6 +17,10 @@ pre-commit = "^3.7.0"
 [tool.poetry.group.dev.dependencies]
 matplotlib = "^3.9.2"
 
+[tool.poetry.urls]
+"Repository Issues" = "https://github.com/Genetic-Evolution-Tournament/issues"
+"Author Homepage" = "https://github.com/AFg6K7h4fhy2"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"