Dependency, Pre-commit, and CI Workflow Improvements - #101

Merged

AndrewSazonov merged 188 commits into

Sep 16, 2025

Commits on Sep 3, 2025

Commits on Sep 5, 2025

Merge branch 'develop' into 14-move-fitresults-out-of-minimizer
AndrewSazonov
committed
034b71f
Merge branch 'develop' into 14-move-fitresults-out-of-minimizer
AndrewSazonov
committed
0ec67fa
Enforces absolute imports for consistency
AndrewSazonov
committed
8de9c8e
Updates pixi.lock
AndrewSazonov
committed
9efddae
Pins dependencies in pixi.toml
AndrewSazonov
committed
e8c63e1
Reorganizes import statements in minimization module
AndrewSazonov
committed
1468c2f

Commits on Sep 6, 2025

Renames and reformats space group lookup dictionary
AndrewSazonov
committed
8245fc2
Improve docstring formatting for consistency
AndrewSazonov
committed
cb1327d

Commits on Sep 7, 2025

Reformats to follow PEP8 line length
AndrewSazonov
committed
6ed94f6

Commits on Sep 8, 2025

Refactors code and updates linting configuration
AndrewSazonov
committed
3760578
Refines change detection logic in progress tracker
AndrewSazonov
committed
f43557f
Simplifies SPDX copyright notice
AndrewSazonov
committed
1f4d1f1
Refactors imports for better organization
AndrewSazonov
committed
86ffb7f
Normalize docstring indentation
AndrewSazonov
committed
63fc095
Adds docstring coverage check with interrogate
AndrewSazonov
committed
77da8eb
Updates docformatter and docstring linting settings
AndrewSazonov
committed
1902e35
Add workflow for code coverage reporting
AndrewSazonov
committed
7b88cb5
Updates pixi.lock
AndrewSazonov
committed
8cfe535
Updates coverage workflow for Codecov integration
AndrewSazonov
committed
878342b
Enhances CI with error handling and detailed logging
AndrewSazonov
committed
a539e3c
Enforces test failure if coverage criteria not met
AndrewSazonov
committed
ef45d5f
Removes forced fail on test failure
AndrewSazonov
committed
9ef9626
Prevent uploads on workflow cancellation
AndrewSazonov
committed
6e35557

Commits on Sep 9, 2025

Merge branch 'develop' into limit-line-length
AndrewSazonov
committed
f8ac85e
Merge branch 'develop' into limit-line-length
AndrewSazonov
committed
ee21206
Refines attribute descriptions in AtomSite class
AndrewSazonov
committed
a16965e
Updates ruff tool configuration temporarily
AndrewSazonov
committed
4b7ca44
Adds coverage task alias in pixi.toml
AndrewSazonov
committed
c150eea
Formats comments in tutorials to follow ruff lint style
AndrewSazonov
committed
c6db27d
Reformats comments in notebook bootstrap script
AndrewSazonov
committed
f4d2506
Refactors peak parameters to use a reference variable
AndrewSazonov
committed
d3fcc78
Compresses space group data into a pickle file
AndrewSazonov
committed
b9d4397
Loosens version constraints for dependencies
AndrewSazonov
committed
915bf65
Add workflow for code complexity analysis
AndrewSazonov
committed
af82ab9
Simplifies GitHub workflow complexity checks
AndrewSazonov
committed
01b498c
Enhances Radon reporting in CI workflow
AndrewSazonov
committed
2a0b2d1
Updates Radon checks to include JSON output
AndrewSazonov
committed
a644a56
Updates Radon checks to use JSON output
AndrewSazonov
committed
09a940f
Enhances complexity report with rankings
AndrewSazonov
committed
e14fba2

Commits on Sep 10, 2025

Refactors PdfFit module handling (N813)
AndrewSazonov
committed
c1aaa27
Refactors mocks in test setup (N806)
AndrewSazonov
committed
1332ae5
Refactors Experiment interface to a class (N802)
AndrewSazonov
committed
6764e74
Adds naming convention checks to linting
AndrewSazonov
committed
2a89488
Adds Bugbear checks to linting configuration
AndrewSazonov
committed
16a6d55
Reorders PEP 8 warnings and comments out Pyupgrade checks
AndrewSazonov
committed
eeb2a9e
Enforces strict checking in zip function calls (B905)
AndrewSazonov
committed
3777449
Simplifies uncertainty attribute check (B009)
AndrewSazonov
committed
0e99520
Replaces parameter access with print statements (B018)
AndrewSazonov
committed
3ab3f4f
Simplifies iteration through mappings (B007)
AndrewSazonov
committed
b5aba32
Fixes argument defaults to avoid function calls (B008)
AndrewSazonov
committed
3ac86e4
Fixes variable override issue in parameter handling (B020)
AndrewSazonov
committed
11f3112
Refactors naming logic in core classes
AndrewSazonov
committed
90a995a
Removes redundant ABC inheritance from Datablock (B024)
AndrewSazonov
committed
37ad809
Improves exception handling clarity (B904)
AndrewSazonov
committed
0f19955
Improves code readability by reformatting and removing extra lines
AndrewSazonov
committed
04d0f42
Refines datablock ID update logic
AndrewSazonov
committed
a1dd854
Reverts to full name for PairDistributionFunction
AndrewSazonov
committed
9bda422
Removes unused asymmetric peak calculations
AndrewSazonov
committed
6ac4f53
Adds TODO for experiment default value processing [ci skip]
AndrewSazonov
committed
2573d35
Refines version formatting in pyproject.toml
AndrewSazonov
committed
b136a4c
Merge branch 'limit-line-length' into code-complexity
AndrewSazonov
committed
e3f6c69
Refines docstring checks and cleans up formatting
AndrewSazonov
committed
38964e9
Add local editable dependencies feature
AndrewSazonov
committed
e896e30
Removes macOS-13 from test matrix
AndrewSazonov
committed
7508616
Removes Python 3.12 support from configuration
AndrewSazonov
committed
7e0cbed
Adds more checks to linter configuration
AndrewSazonov
committed
fefdc1e
Removes Python 3.12 environment configurations
AndrewSazonov
committed
d49e85f
Updates Ruff lint rules and ignores for clarity
AndrewSazonov
committed
725aa3d
Adds GitHub workflow for branch badge summary
AndrewSazonov
committed
ef7a8bf
Standardizes badge reference formatting
AndrewSazonov
committed
ac21347
Remove backticks from branch names in badge table
AndrewSazonov
committed
6d5db03
Excludes specific directories from CodeFactor analysis
AndrewSazonov
committed
b5488bb
Adds and removes CodeFactor configuration file
AndrewSazonov
committed
e8fc0c9
Removes CodeFactor configuration file
AndrewSazonov
committed
3887e25
Adds comprehensive badge summary workflow
AndrewSazonov
committed
f6ca9ed
Renames YAML files and updates badge summary logic
AndrewSazonov
committed
9c8ebe9
Update badge links in GitHub workflow
AndrewSazonov
committed
048e733
Corrects YAML file extension for build-docs links
AndrewSazonov
committed
0e9dd4e
Refactors badge generation to use Python script
AndrewSazonov
committed
db2d306
Add badge generation script for markdown documentation
AndrewSazonov
committed
b2b0a3b
Enhances badge generation with complexity metrics
AndrewSazonov
committed
2fc0fc2
Enhances branch analysis workflow with git worktrees
AndrewSazonov
committed
6d21e29
Updates checkout action to fetch full history
AndrewSazonov
committed
be85605
Adds manifest-path setup for pixi action
AndrewSazonov
committed
0e4a020
Copies necessary files for worktree operations
AndrewSazonov
committed
3f05f7c
Removes manifest-path from pixi setup
AndrewSazonov
committed
8b24238
Adds manifest path to pixi run commands
AndrewSazonov
committed
87b826b
Switches to environment variable for manifest path
AndrewSazonov
committed
a4ae52a
Fixes environment variable syntax in workflow
AndrewSazonov
committed
5501e31
Simplifies badge workflow execution process
AndrewSazonov
committed
7905ca7
Consolidates branch-specific code checks
AndrewSazonov
committed
8ac62ac
Enhances workflow to support multiple branches
AndrewSazonov
committed
132fca7
Improve badge workflow for branch handling
AndrewSazonov
committed
4cadc7b
Removes redundant git worktree command
AndrewSazonov
committed
8c62d3e
Adds concurrency control and logging to workflow
AndrewSazonov
committed
05c85aa
Enhances branch analysis logging and excludes file
AndrewSazonov
committed
eaf185c
Refactors badge generation and updates YAML for dynamic naming
AndrewSazonov
committed
12ea391
Replaces shell variable with GitHub Actions syntax
AndrewSazonov
committed
3381031
Refines badge generation logic for complexity and maintainability
AndrewSazonov
committed
52ba3ce
Update docstring coverage badge links
AndrewSazonov
committed
04b2e34
Updates dependencies: ruff to v0.13.0, libcxx to v21.1.1
AndrewSazonov
committed
785d7db
Refines badge generation workflow and removes BADGES.md
AndrewSazonov
committed
05ca77b

Commits on Sep 11, 2025

Commits on Sep 12, 2025

Replaces badge generation script with GitHub Actions workflow
AndrewSazonov
committed
8ef0513
Exclude specific file from radon analysis; remove badgery
AndrewSazonov
committed
9416725
Adds Badgery configuration for CI/CD and code quality
AndrewSazonov
committed
6eb8018
Updates security workflow filename in config
AndrewSazonov
committed
f26da35
Adds a step to display package info before execution
AndrewSazonov
committed
f3814a2
Adds config option to badgery execution
AndrewSazonov
committed
0dd9e34
Adds documentation build and deployment action
AndrewSazonov
committed
34ef4f3
Updates workflow to use dynamic publish branch
AndrewSazonov
committed
b4201d0
Refines .badgery.yaml configurations
AndrewSazonov
committed
e56bd9d
Removes security scan workflow
AndrewSazonov
committed
d65c170
Rename workflow for dashboard build and publish
AndrewSazonov
committed
cf30f3d
Merge remote-tracking branch 'origin/develop' into code-complexity
AndrewSazonov
committed
a8cb71b
Updates dependencies
AndrewSazonov
committed
c61529b

Commits on Sep 13, 2025

Adds comprehensive 'all' dependency grouping
AndrewSazonov
committed
6995eba
Refines dependency management in configuration
AndrewSazonov
committed
3ca90ba
Clarifies comments for dependency descriptions
AndrewSazonov
committed
6fc9f3c

Commits on Sep 14, 2025

Update dependencies
AndrewSazonov
committed
14106e6
Reactivates argument-related linter checks
AndrewSazonov
committed
125678f
Updates pixi command options in workflows
AndrewSazonov
committed
866b02d
Add pre-commit configuration and update dependencies
AndrewSazonov
committed
458347b
Updates pre-commit configuration and tasks
AndrewSazonov
committed
74498f8
Add pre-commit hooks to manage pixi.lock sha256 changes
AndrewSazonov
committed
089331f
Refactor pixi.lock handling and update pre-commit configuration
AndrewSazonov
committed
6518e15
Adds pre-commit autoupdate command
AndrewSazonov
committed
31a3465
Removes wheel/pixi.toml configuration file
AndrewSazonov
committed
f71bcfd
Updates pre-commit setup and adds dev-setup dependency
AndrewSazonov
committed
3585557

Commits on Sep 15, 2025

Updates pixi.toml with refined configurations
AndrewSazonov
committed
1d016ad
Refactor task dependencies in pixi.toml for clarity and consistency
AndrewSazonov
committed
2c63b7f
Refactor easydiffraction dependency and update development tasks in pixi.toml
AndrewSazonov
committed
f167089
Enhances GitHub Actions workflows
AndrewSazonov
committed
dca60a8
Update workflow setups to use default environments
AndrewSazonov
committed
81aa5e8
Remove unused GitHub workflows and update CI configuration
AndrewSazonov
committed
4cb261d
Refines version formatting and updates dev install
AndrewSazonov
committed
fb29932
Update zstandard package to version 0.25.0
AndrewSazonov
committed
99bd992
Handles missing environment variables gracefully
AndrewSazonov
committed
76e2164
Revamps testing workflow; simplifies steps
AndrewSazonov
committed
b143397
Move code quality checks out and enhance testing workflows
AndrewSazonov
committed
86220a4
Refines PYTHONPATH handling and updates dependencies
AndrewSazonov
committed
b599f46
Adds notebook formatting checks to CI workflow
AndrewSazonov
committed
3fcf9ba
Standardizes and renames GitHub workflows
AndrewSazonov
committed
ba846c8
Refactors workflow filenames and updates dependencies
AndrewSazonov
committed
2cb0ad9
Enhances PyPI workflow with push trigger and extras
AndrewSazonov
committed
bd7f018
Updates GitHub workflows and removes redundant config
AndrewSazonov
committed
40b3fc4
Update branch handling in CI workflow
AndrewSazonov
committed
7f9157d
Simplifies environment variable usage in workflows
AndrewSazonov
committed
f36b8be
Adds setup for development dependencies and refines tests
AndrewSazonov
committed
83ba361
Enhances workflow with version check and expanded triggers
AndrewSazonov
committed
dd7e3fd
Updates development setup and pre-commit checks
AndrewSazonov
committed
2b9bd4b
Refines code for simplification and consistency following `SIM` rules
AndrewSazonov
committed
7fcfe07
Replaces os.path with pathlib for file handling following `PTH` rule
AndrewSazonov
committed
62a511d
Improve pathlib usage and enhance security checks
AndrewSazonov
committed
49862e3
Refines GitHub workflow triggers
AndrewSazonov
committed
fa5c217
Corrects typo in secret token variable names
AndrewSazonov
committed
cf5e253
Ensure cross-platform path consistency in tests
AndrewSazonov
committed
2ad7935
Enables `PGH` checks in linting configuration
AndrewSazonov
committed
09f4db2
Combines IPython check with 'easydiffraction' spec
AndrewSazonov
committed
cbbdac4
Update pixi environment settings to default
AndrewSazonov
committed
f6eaf54
Adds import convention checks to linter `ICN`
AndrewSazonov
committed
eb3adbe
Refines config and docstring for clarity
AndrewSazonov
committed
736a2ac
Expands docs workflow trigger to all branches
AndrewSazonov
committed
969550c
Removes automatic release trigger on push
AndrewSazonov
committed
0136571
Updates workflows for main branch compatibility
AndrewSazonov
committed
4bee3a5
Adds pre-push hook to pre-commit checks
AndrewSazonov
committed
b5d53a1
Updates pre-commit to use staged checks
AndrewSazonov
committed
d31b763
Refactors format check command sequence
AndrewSazonov
committed
2462187
Updates GitHub Actions triggers and job naming
AndrewSazonov
committed
30232ae
Simplifies workflow trigger configuration
AndrewSazonov
committed
9e6b7f0
Refines test and build action titles
AndrewSazonov
committed
e352d2c
Rename workflow job names for clarity
AndrewSazonov
committed
dfb59f6
Updates title for clarity in radon metrics
AndrewSazonov
committed
54fb645
Updates test and code quality titles for clarity
AndrewSazonov
committed
5385500

Commits on Sep 16, 2025

Renames workflow files for clarity
AndrewSazonov
committed
82a916a
Enhances CI workflow for code quality log formatting
AndrewSazonov
committed
2710201
Improves summary table formatting
AndrewSazonov
committed
37fa3a3
Merge branch 'develop' into ruff-lint-arg
AndrewSazonov
committed
82afe1b
Updates workflow step name for clarity [ci skip]
AndrewSazonov
committed
b8c3cec
Enhances version flag handling in CLI
AndrewSazonov
committed
3a1f962