kohgpjax 0.4.2__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (46) hide show
  1. kohgpjax-0.4.2/.github/ISSUE_TEMPLATE/bug_report.yml +63 -0
  2. kohgpjax-0.4.2/.github/ISSUE_TEMPLATE/config.yml +2 -0
  3. kohgpjax-0.4.2/.github/ISSUE_TEMPLATE/documentation.yml +27 -0
  4. kohgpjax-0.4.2/.github/ISSUE_TEMPLATE/feature_request.yml +34 -0
  5. kohgpjax-0.4.2/.github/ISSUE_TEMPLATE/question.yml +24 -0
  6. kohgpjax-0.4.2/.github/workflows/docs.yml +48 -0
  7. kohgpjax-0.4.2/.github/workflows/release.yml +37 -0
  8. kohgpjax-0.4.2/.github/workflows/tests.yml +41 -0
  9. kohgpjax-0.4.2/.gitignore +18 -0
  10. kohgpjax-0.4.2/.nojekyll +0 -0
  11. kohgpjax-0.4.2/LICENSE.md +614 -0
  12. kohgpjax-0.4.2/PKG-INFO +322 -0
  13. kohgpjax-0.4.2/README.md +280 -0
  14. kohgpjax-0.4.2/docs/LICENSE.md +3 -0
  15. kohgpjax-0.4.2/docs/_examples/basics.md +255 -0
  16. kohgpjax-0.4.2/docs/_examples/basics_files/basics_8_0.png +0 -0
  17. kohgpjax-0.4.2/docs/_examples/data/field.csv +100 -0
  18. kohgpjax-0.4.2/docs/_examples/data/sim.csv +500 -0
  19. kohgpjax-0.4.2/docs/index.md +221 -0
  20. kohgpjax-0.4.2/docs/installation.md +9 -0
  21. kohgpjax-0.4.2/docs/javascripts/katex.js +10 -0
  22. kohgpjax-0.4.2/docs/scripts/gen_examples.py +102 -0
  23. kohgpjax-0.4.2/docs/scripts/gen_pages.py +90 -0
  24. kohgpjax-0.4.2/docs/scripts/notebook_converter.py +30 -0
  25. kohgpjax-0.4.2/examples/basics.py +234 -0
  26. kohgpjax-0.4.2/examples/data/field.csv +100 -0
  27. kohgpjax-0.4.2/examples/data/sim.csv +500 -0
  28. kohgpjax-0.4.2/kohgpjax/__init__.py +18 -0
  29. kohgpjax-0.4.2/kohgpjax/dataset.py +139 -0
  30. kohgpjax-0.4.2/kohgpjax/gps.py +496 -0
  31. kohgpjax-0.4.2/kohgpjax/kernels/__init__.py +0 -0
  32. kohgpjax-0.4.2/kohgpjax/kernels/computations/__init__.py +0 -0
  33. kohgpjax-0.4.2/kohgpjax/kernels/computations/kohcomputation.py +76 -0
  34. kohgpjax-0.4.2/kohgpjax/kernels/kohkernel.py +45 -0
  35. kohgpjax-0.4.2/kohgpjax/kohmodel.py +278 -0
  36. kohgpjax-0.4.2/kohgpjax/parameters.py +287 -0
  37. kohgpjax-0.4.2/mkdocs.yml +106 -0
  38. kohgpjax-0.4.2/pyproject.toml +205 -0
  39. kohgpjax-0.4.2/tests/conftest.py +19 -0
  40. kohgpjax-0.4.2/tests/integration/test_integration_posterior_density.py +196 -0
  41. kohgpjax-0.4.2/tests/kernels/test_kohcomputation.py +247 -0
  42. kohgpjax-0.4.2/tests/kernels/test_kohkernel.py +96 -0
  43. kohgpjax-0.4.2/tests/test_dataset.py +414 -0
  44. kohgpjax-0.4.2/tests/test_gps.py +304 -0
  45. kohgpjax-0.4.2/tests/test_kohmodel.py +528 -0
  46. kohgpjax-0.4.2/tests/test_parameters.py +502 -0
@@ -0,0 +1,63 @@
1
+ ---
2
+ name: Bug Report
3
+ description: Create a Report to Help us Improve
4
+ labels:
5
+ - bug
6
+ body:
7
+ - id: describe
8
+ type: textarea
9
+ attributes:
10
+ label: Describe the Bug
11
+ description: A clear and concise description of what the bug is.
12
+ validations:
13
+ required: true
14
+ - id: reproduce
15
+ type: textarea
16
+ attributes:
17
+ label: To Reproduce
18
+ description: >-
19
+ A minimal working example of code to reproduce the unexpected behaviour,
20
+ this will render as `Python` code so no need for backticks.
21
+ value: |-
22
+ import kohgpjax
23
+
24
+ ...
25
+ render: Python
26
+ validations:
27
+ required: true
28
+ - id: expected
29
+ type: textarea
30
+ attributes:
31
+ label: Expected Behaviour
32
+ description: >-
33
+ A clear and concise description of what you expected to happen.
34
+ validations:
35
+ required: true
36
+ - id: actual
37
+ type: textarea
38
+ attributes:
39
+ label: Actual Behaviour
40
+ description: >-
41
+ Be a specific and detailed as you can. Paste any output or stack traces
42
+ of errors you receive.
43
+ validations:
44
+ required: true
45
+ - id: version
46
+ type: input
47
+ attributes:
48
+ label: Version In Use
49
+ description: |-
50
+ Can be found by
51
+ ```sh
52
+ python -c "import kohgpjax; print(kohgpjax.__version__)"
53
+ ```
54
+ validations:
55
+ required: true
56
+ - id: additional
57
+ type: textarea
58
+ attributes:
59
+ label: Additional Context
60
+ value: |-
61
+ - Python version:
62
+ - Operating system:
63
+ render: Markdown
@@ -0,0 +1,2 @@
1
+ ---
2
+ blank_issues_enabled: false
@@ -0,0 +1,27 @@
1
+ ---
2
+ name: Documentation
3
+ description: How Can We Improve the Documentation
4
+ labels:
5
+ - documentation
6
+ body:
7
+ - id: section
8
+ type: textarea
9
+ attributes:
10
+ label: Which Section of the Documentation Needs Improving?
11
+ description: Please provide a link (if it is a specific page).
12
+ validations:
13
+ required: true
14
+ - id: problem
15
+ type: textarea
16
+ attributes:
17
+ label: What Can be Improved About This Section
18
+ description: Is it incomplete, incorrect or difficult to understand?
19
+ validations:
20
+ required: true
21
+ - id: suggestions
22
+ type: textarea
23
+ attributes:
24
+ label: How to Improve This Section
25
+ description: >-
26
+ Do you have any specific suggestions we could take to improve the
27
+ documentation?
@@ -0,0 +1,34 @@
1
+ ---
2
+ name: Feature Request
3
+ description: Suggest a Way to Improve This Project
4
+ labels:
5
+ - enhancement
6
+ body:
7
+ - id: problem
8
+ type: textarea
9
+ attributes:
10
+ label: Is Your Feature Request Related to a Problem? Please Describe
11
+ description: A clear and concise description of what the problem is.
12
+ placeholder: I'm always frustrated when [...]
13
+ validations:
14
+ required: true
15
+ - id: solution
16
+ type: textarea
17
+ attributes:
18
+ label: Describe the Solution You'd Like
19
+ description: A clear and concise description of what you want to happen.
20
+ validations:
21
+ required: true
22
+ - id: alternatives
23
+ type: textarea
24
+ attributes:
25
+ label: Describe Alternatives You've Considered
26
+ description: >-
27
+ A clear and concise description of any alternative solutions or features
28
+ you've considered.
29
+ - id: additional
30
+ type: textarea
31
+ attributes:
32
+ label: Additional Context
33
+ description: >-
34
+ Add any other context or screenshots about the feature request here.
@@ -0,0 +1,24 @@
1
+ ---
2
+ name: Question
3
+ description: General Questions About Using KOH-GPJax
4
+ labels:
5
+ - question
6
+ body:
7
+ - id: topic
8
+ type: dropdown
9
+ attributes:
10
+ label: What is the Topic of Your Question
11
+ description: Please indicate the topic in the title of your question.
12
+ options:
13
+ - Documentation
14
+ - Installation
15
+ - Usage
16
+ - Other
17
+ validations:
18
+ required: true
19
+ - id: question
20
+ type: textarea
21
+ attributes:
22
+ label: Add Your Question Below
23
+ validations:
24
+ required: true
@@ -0,0 +1,48 @@
1
+ name: Documentation
2
+
3
+ on:
4
+ push:
5
+ branches:
6
+ - main
7
+ pull_request:
8
+
9
+ jobs:
10
+ docs:
11
+ permissions:
12
+ contents: write # Required to publish documentation to GitHub Pages
13
+ runs-on: ubuntu-latest
14
+ steps:
15
+ - name: Checkout source
16
+ uses: actions/checkout@v6
17
+
18
+ - name: Cache tox
19
+ uses: actions/cache@v5
20
+ with:
21
+ path: .tox
22
+ key: tox-${{ hashFiles('pyproject.toml') }}
23
+
24
+ - name: Set up Python
25
+ uses: actions/setup-python@v6
26
+ with:
27
+ python-version: "3.12" # "3.x"
28
+ cache: "pip"
29
+ cache-dependency-path: "pyproject.toml"
30
+
31
+ - name: Install tox
32
+ run: python -m pip install tox
33
+ - name: Build HTML documentation with tox
34
+ run: tox -e docs
35
+
36
+ # Automatically deploy documentation to a GitHub Pages website on pushing to main.
37
+ # Requires configuring the repository to deploy GitHub pages from a branch
38
+ # gh-pages (https://tinyurl.com/gh-pages-from-branch), which will be created the
39
+ # first time this workflow step is run.
40
+ - name: Publish documentation on GitHub pages
41
+ if: success() && github.event_name != 'pull_request'
42
+ uses: peaceiris/actions-gh-pages@4f9cc6602d3f66b9c108549d475ec49e8ef4d45e # v4
43
+ with:
44
+ github_token: ${{ secrets.GITHUB_TOKEN }}
45
+ publish_dir: site
46
+ publish_branch: gh-pages
47
+ user_name: "github-actions[bot]"
48
+ user_email: "github-actions[bot]@users.noreply.github.com"
@@ -0,0 +1,37 @@
1
+ name: Release
2
+
3
+ on:
4
+ push:
5
+ tags:
6
+ - "v*.*.*"
7
+
8
+ permissions:
9
+ contents: write
10
+
11
+ jobs:
12
+ release:
13
+ runs-on: ubuntu-latest
14
+ environment: pypi
15
+ permissions:
16
+ contents: write
17
+ id-token: write
18
+
19
+ steps:
20
+ - uses: actions/checkout@v6
21
+
22
+ - uses: actions/setup-python@v6
23
+ with:
24
+ python-version: "3.12"
25
+
26
+ - run: python -m pip install build
27
+ - run: python -m build
28
+
29
+ - uses: pypa/gh-action-pypi-publish@release/v1
30
+
31
+ - name: Create GitHub Release
32
+ env:
33
+ GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
34
+ run: |
35
+ gh release create "$GITHUB_REF_NAME" dist/* \
36
+ --title "$GITHUB_REF_NAME" \
37
+ --generate-notes
@@ -0,0 +1,41 @@
1
+ name: Tests
2
+
3
+ on:
4
+ push:
5
+ branches:
6
+ - main
7
+ pull_request:
8
+ paths-ignore:
9
+ - "**.md"
10
+
11
+ jobs:
12
+ tests:
13
+ runs-on: ubuntu-latest
14
+ strategy:
15
+ matrix:
16
+ python-version:
17
+ - "3.11"
18
+ - "3.12"
19
+
20
+ steps:
21
+ - name: Checkout source
22
+ uses: actions/checkout@v6
23
+
24
+ - name: Cache tox
25
+ uses: actions/cache@v5
26
+ with:
27
+ path: .tox
28
+ key: tox-${{hashFiles('pyproject.toml') }}
29
+
30
+ - name: Set up python
31
+ uses: actions/setup-python@v6
32
+ with:
33
+ python-version: ${{ matrix.python-version }}
34
+ cache: pip
35
+ cache-dependency-path: pyproject.toml
36
+
37
+ - name: Install dependencies
38
+ run: python -m pip install tox tox-gh
39
+
40
+ - name: Test with tox
41
+ run: tox run
@@ -0,0 +1,18 @@
1
+ __pycache__
2
+ .vscode
3
+ build/
4
+ .pytest_cache/
5
+
6
+ kohgpjax.egg-info/
7
+
8
+ .coverage*
9
+ coverage.xml
10
+
11
+ environment.yml
12
+ uv.lock
13
+
14
+ *.npz
15
+ *.npy
16
+
17
+ .tox
18
+ site/
File without changes