GEOPY-3101: Update toml to latest format

.codespellignore

@@ -1,2 +1,3 @@
 ba
 nd
+astroid

.github/dependabot.yml

@@ -0,0 +1,33 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    target-branch: "develop"
+    schedule:
+      interval: "weekly"
+    cooldown:
+      default-days: 1
+    groups:
+      github-actions:
+        patterns:
+          - actions/*
+      mirageo-ci-tools:
+        patterns:
+          - MiraGeoscience/CI-tools/.github/actions/*
+          - MiraGeoscience/CI-tools/.github/workflows/*
+  - package-ecosystem: "pre-commit"
+    directory: "/"
+    target-branch: "develop"
+    schedule:
+      interval: "weekly"
+    cooldown:
+      default-days: 1
+    groups:
+      pre-commit-hooks:
+        patterns:
+          - "*"

.github/workflows/dependabot-auto-merge.yml

@@ -0,0 +1,16 @@
+name: Dependabot auto-merge
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+jobs:
+  call-workflow-dependabot-auto-merge:
+    uses: MiraGeoscience/CI-tools/.github/workflows/reusable-dependabot-auto-merge.yml@9e46551783cee8a8c2c7a30794af4b98e2671729 # v3.13.6
+    permissions:
+      contents: write
+      pull-requests: write
+      statuses: write
+      checks: read
+    with:
+      dependabot-groups: mirageo-ci-tools,pre-commit-hooks

.github/workflows/pr_jira_actions.yml

@@ -0,0 +1,17 @@
+name: JIRA actions
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review, edited]
+
+jobs:
+  call-workflow-pr_jira_actions:
+    uses: MiraGeoscience/CI-tools/.github/workflows/reusable-jira-pr_actions.yml@9e46551783cee8a8c2c7a30794af4b98e2671729 # v3.13.6
+    permissions:
+      contents: read
+      pull-requests: write
+      statuses: write
+    secrets:
+      JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN }}
+      JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }}
+      JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }}

.github/workflows/security_scan.yml

@@ -0,0 +1,42 @@
+name: Security Scan
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    branches:
+      - develop
+      - main
+      - release/**
+      - feature/**
+      - hotfix/**
+  push:
+    branches:
+      - develop
+      - main
+      - release/**
+      - feature/**
+      - hotfix/**
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions: {}
+
+jobs:
+  call-workflow-zizmor-annotate:
+    name: Zizmor analysis (annotate)
+    if: ${{ github.event_name == 'pull_request' }}
+    permissions:
+      checks: write
+      contents: read
+      actions: read
+    uses: MiraGeoscience/CI-tools/.github/workflows/reusable-zizmor-annotate.yml@9e46551783cee8a8c2c7a30794af4b98e2671729 # v3.13.6
+
+  call-workflow-zizmor:
+    name: Zizmor analysis
+    if: ${{ github.event_name != 'pull_request' }}
+    permissions:
+      contents: read
+      actions: read
+    uses: MiraGeoscience/CI-tools/.github/workflows/reusable-zizmor-security.yml@9e46551783cee8a8c2c7a30794af4b98e2671729 # v3.13.6

.github/workflows/static_analysis.yml

@@ -0,0 +1,31 @@
+name: Static analysis
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    branches:
+      - develop
+      - main
+      - release/**
+      - feature/**
+      - hotfix/**
+  push:
+    branches:
+      - develop
+      - main
+      - release/**
+      - feature/**
+      - hotfix/**
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  call-workflow-pre-commit:
+    name: Pre-Commit
+    uses: MiraGeoscience/CI-tools/.github/workflows/reusable-pre_commit.yml@9e46551783cee8a8c2c7a30794af4b98e2671729 # v3.13.6
+    permissions:
+      contents: read
+    with:
+      python-version: "3.12"

.github/workflows/wip-status.yml

@@ -0,0 +1,12 @@
+name: WIP status
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review, edited]
+
+jobs:
+  call-workflow-wip-status:
+    uses: MiraGeoscience/CI-tools/.github/workflows/reusable-wip-status.yml@9e46551783cee8a8c2c7a30794af4b98e2671729 # v3.13.6
+    permissions:
+      contents: read
+      statuses: write

.pre-commit-config.yaml

@@ -11,11 +11,6 @@ ci:
     autoupdate_schedule: quarterly
 
 repos:
--   repo: https://github.com/python-poetry/poetry
-    rev: 2.4.1
-    hooks:
-    -   id: poetry-check
-        args: [--lock, --no-plugins]
 -   repo: https://github.com/hadialqattan/pycln
     rev: v2.6.0
     hooks:
@@ -41,22 +36,7 @@ repos:
             types-toml,
             types-PyYAML,
         ]
-        exclude: |
-            (?x)(^
-                geoh5py/interfaces/__init__.py|
-                geoh5py/handlers/__init__.py|
-                geoh5py/interfaces/.*|
-                geoh5py/handlers/.*|
-                tests/.*|
-                geoh5py/shared/utils.py|
-                geoh5py/shared/entity_type.py|
-                geoh5py/data/data_type.py|
-                geoh5py/objects/cell_object.py|
-                geoh5py/shared/concatenation/drillhole.py|
-                geoh5py/shared/concatenation/concatenator.py|
-                geoh5py/workspace/workspace.py|
-                geoh5py/ui_json/validation.py
-            )$
+        exclude: ^tests/
 -   repo: https://github.com/codingjoe/relint
     rev: 3.3.1
     hooks:
@@ -66,25 +46,24 @@ repos:
     rev: v1.1.0
     hooks:
     -   id: check-copyright
-        entry: python devtools/check-copyright.py
-        exclude: (^\.|\.yml|\.toml|^setup.py$|(docs|assets|environments)/)
+        files: (^LICENSE|^README(|-dev)\.rst|\.py|\.pyi)$
+        exclude: (^\.|^docs/|^assets/)
     -   id: prepare-commit-msg
     -   id: check-commit-msg
 -   repo: local
     hooks:
     -   id: pylint
         name: pylint
-        entry: poetry run pylint
+        entry: .\\devtools\\conda_env_pylint.bat
         language: system
         require_serial: true  # pylint does its own parallelism
-        types: [text]
-        types_or: [python, pyi]
-        exclude: ^(devtools|docs|geoh5py/interfaces|geoh5py/handlers)/
+        types: [python]
+        exclude: ^(devtools|docs)/
 -   repo: https://github.com/codespell-project/codespell
     rev: v2.4.2
     hooks:
     -   id: codespell
-        exclude: (\.lock|\.ipynb|^THIRD_PARTY_SOFTWARE\.rst)$
+        exclude: (\.lock|\.ipynb|\.bib|^THIRD_PARTY_SOFTWARE\.rst)$
         entry: codespell -I .codespellignore
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0

assets/mag_dipole_app.py

@@ -107,7 +107,9 @@ def vectorize(entity):
     # Loop over the dipoles
     fields = np.zeros_like(observations)
 
-    for source, moment, inclination, declination in zip(dipoles, mom, inc, dec):
+    for source, moment, inclination, declination in zip(
+        dipoles, mom, inc, dec, strict=True
+    ):
         fields += b_field(source, observations, moment, inclination, declination)
 
     tmi = tmi_projection(fields, (earth_inc, earth_dec))

assets/training/0-core.ipynb

@@ -283,4 +283,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

assets/training/1-collections.ipynb

@@ -308,6 +308,7 @@
    "source": [
     "import numpy as np\n",
     "\n",
+    "\n",
     "array = np.array([[1, 2, 3], [4, 5, 6]])  # Create a 2D array\n",
     "array.sum(axis=0)"
    ]
@@ -382,4 +383,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

assets/training/2-functions.ipynb

@@ -351,4 +351,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

assets/training/3-classes.ipynb

@@ -252,4 +252,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

assets/training/4-modules.ipynb

@@ -83,4 +83,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}