Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
86 commits
Select commit Hold shift + click to select a range
f447867
upgrade to latest linkml
realmarcin Mar 17, 2023
a324f30
Merge pull request #12 from bridge2ai/cookiecutter
realmarcin Mar 18, 2023
52090da
Merge branch 'schema-edits'
realmarcin Mar 28, 2023
b5daf34
Update README.md
realmarcin Jun 21, 2023
f5ca8c9
Update README.md
realmarcin Aug 14, 2023
cd9837d
Update README.md
realmarcin Aug 14, 2023
3e96d2f
Update README.md
realmarcin Aug 14, 2023
82895eb
Update README.md
realmarcin Apr 8, 2025
97643a5
Enhance LinkML schema to 100% Google MCT coverage with HuggingFace an…
realmarcin Nov 20, 2025
00936c4
Add alignment analysis and harmonized schema proposal for datasheets …
realmarcin Nov 21, 2025
1ce7754
Update CLAUDE.md with harmonization analysis and schema information
realmarcin Nov 23, 2025
432ca7a
Implement Phase 1 datasheets integration with practical examples and …
realmarcin Nov 23, 2025
f562a43
Complete Phases 2-4: Migration utilities, validation tools, and compr…
realmarcin Nov 23, 2025
0c5dad0
Merge pull request #18 from bridge2ai/schema-update
realmarcin Nov 23, 2025
0c04448
Extend LinkML schema with 100% KOGUT template coverage for DOE scient…
realmarcin Nov 23, 2025
314724e
Fix deprecated GitHub Actions versions in test workflow
realmarcin Nov 23, 2025
5a53132
Fix deprecated GitHub Actions versions in test workflow
realmarcin Nov 23, 2025
8bfb0cd
Add KOGUT template source files and update gitignore
realmarcin Nov 23, 2025
54ebef5
Update src/linkml/modelcards.yaml
realmarcin Nov 23, 2025
d4baa5c
Update src/data/examples/kogut/climate-model-kogut.yaml
realmarcin Nov 23, 2025
7b23d27
Update src/linkml/modelcards.yaml
realmarcin Nov 23, 2025
fec2929
Update src/data/examples/kogut/README.md
realmarcin Nov 23, 2025
25c0db0
Update src/data/examples/kogut/climate-model-kogut.yaml
realmarcin Nov 23, 2025
4f13a00
Update src/data/examples/kogut/climate-model-kogut.yaml
realmarcin Nov 23, 2025
6c07691
Update src/data/examples/kogut/README.md
realmarcin Nov 23, 2025
37eef9e
Update src/data/examples/kogut/README.md
realmarcin Nov 23, 2025
0a34e21
Initial plan
Copilot Nov 23, 2025
13cc800
Initial plan
Copilot Nov 23, 2025
1606602
Update src/linkml/modelcards.yaml
realmarcin Nov 23, 2025
0f633b2
Update src/linkml/modelcards.yaml
realmarcin Nov 23, 2025
6a00750
Change orcid field from string to uri range for consistency
Copilot Nov 23, 2025
9bd9daf
Initial plan
Copilot Nov 23, 2025
1af2022
Make training_data_separate and evaluation_data_separate boolean glob…
Copilot Nov 23, 2025
8234110
Fix evaluation_data_separate global slot to be boolean type
Copilot Nov 23, 2025
aa84b59
Fix Poetry package configuration and CI installation issues
realmarcin Nov 23, 2025
c9a0ad7
Fix Poetry package configuration and CI installation issues
realmarcin Nov 23, 2025
39aec46
Fix schema path references in about.yaml and Makefile
realmarcin Nov 23, 2025
226da56
Fix schema path references in about.yaml and Makefile
realmarcin Nov 23, 2025
d29b999
Fix test module import errors in test_data.py
realmarcin Nov 23, 2025
8542169
Fix test module import errors in test_data.py
realmarcin Nov 23, 2025
861cae5
Fix firewall blocking Poetry installation by using pre-installed version
realmarcin Nov 23, 2025
63be82e
Fix firewall blocking Poetry installation by using pre-installed version
realmarcin Nov 23, 2025
d00605f
Install Poetry via pip instead of pre-installed version
realmarcin Nov 23, 2025
a59f54c
Install Poetry via pip instead of pre-installed version
realmarcin Nov 23, 2025
05b8c6f
Fix Makefile to use poetry install --no-root
realmarcin Nov 23, 2025
8f00514
Fix Makefile to use poetry install --no-root
realmarcin Nov 23, 2025
7d5eda3
Fix Makefile to use poetry install --no-root
realmarcin Nov 23, 2025
9ed3a79
Fix deploy_documentation.yml to use --no-root flag
realmarcin Nov 23, 2025
7e6b6b6
Fix deploy_documentation.yml to use --no-root flag
realmarcin Nov 23, 2025
76fad70
Fix deploy_documentation.yml to use --no-root flag
realmarcin Nov 23, 2025
ba78ed3
Update Python version from 3.9 to 3.12 in test workflow
realmarcin Nov 23, 2025
e04cca2
Update Python version from 3.9 to 3.12 in test workflow
realmarcin Nov 23, 2025
bf07991
Update Python version from 3.9 to 3.12 in test workflow
realmarcin Nov 23, 2025
b5e775f
Fix missing --no-root flag in PyPI publish workflow
realmarcin Nov 23, 2025
f160469
Fix missing --no-root flag in PyPI publish workflow
realmarcin Nov 23, 2025
1f9a0f7
Fix missing --no-root flag in PyPI publish workflow
realmarcin Nov 23, 2025
571211c
Update schema: separate base and extended slots, rename KOGUT to exte…
Copilot Nov 23, 2025
6a445b0
Rename kogut directory and files to extended, update all references
Copilot Nov 23, 2025
ce1cad5
Clarify KOGUT path reference is for original template source
Copilot Nov 23, 2025
639bbc4
Update test to look for extended template examples instead of kogut
realmarcin Nov 23, 2025
64cff55
Fix CI/CD: Python 3.12, --no-root flags, and pyproject.toml deprecation
realmarcin Nov 23, 2025
35c65ae
Fix CI/CD: Python 3.12, --no-root flags, and pyproject.toml deprecation
realmarcin Nov 23, 2025
c3b7a40
Fix CI/CD: Python 3.12, --no-root flags, and pyproject.toml deprecation
realmarcin Nov 23, 2025
e947968
Merge main into schema-extend, keeping 'extended' terminology
realmarcin Nov 23, 2025
e3dd67c
Update PyYAML to 6.0.3 for Python 3.12 compatibility
realmarcin Nov 23, 2025
5e2093c
Update PyYAML to 6.0.3 for Python 3.12 compatibility
realmarcin Nov 23, 2025
12be021
Update PyYAML to 6.0.3 for Python 3.12 compatibility
realmarcin Nov 23, 2025
17e4c66
Update PyYAML to 6.0.3 for Python 3.12 compatibility
realmarcin Nov 23, 2025
d6665a1
Update PyYAML to 6.0.3 for Python 3.12 compatibility
realmarcin Nov 23, 2025
a753ac8
Update PyYAML to 6.0.3 for Python 3.12 compatibility
realmarcin Nov 23, 2025
54e09cb
Update greenlet to 3.2.4 for Python 3.12 compatibility
realmarcin Nov 23, 2025
d4600ad
Update greenlet to 3.2.4 for Python 3.12 compatibility
realmarcin Nov 23, 2025
0ae032d
Update greenlet to 3.2.4 for Python 3.12 compatibility
realmarcin Nov 23, 2025
2d638b4
Update greenlet to 3.2.4 for Python 3.12 compatibility
realmarcin Nov 23, 2025
a359ad2
Update greenlet to 3.2.4 for Python 3.12 compatibility
realmarcin Nov 23, 2025
8477dcd
Update greenlet to 3.2.4 for Python 3.12 compatibility
realmarcin Nov 23, 2025
7c2429d
Merge pull request #20 from bridge2ai/copilot/sub-pr-19
realmarcin Nov 23, 2025
98604ec
Merge pull request #21 from bridge2ai/copilot/sub-pr-19-again
realmarcin Nov 23, 2025
8dc97a9
Merge pull request #22 from bridge2ai/copilot/sub-pr-19-another-one
realmarcin Nov 23, 2025
6b5fd78
Merge pull request #19 from bridge2ai/schema-extend
realmarcin Nov 23, 2025
afd93f3
Move schema files to cookiecutter standard locations
realmarcin Nov 23, 2025
1ea1549
Move schema to correct cookiecutter standard path
realmarcin Nov 23, 2025
7fe4a47
Merge main into schema-update: resolve schema path conflicts
realmarcin Nov 23, 2025
436a87c
Complete Phase 1 D4D harmonization with external reference pattern
realmarcin Nov 24, 2025
8545db5
Remove .DS_Store files from repository
realmarcin Nov 24, 2025
157f940
Merge pull request #24 from bridge2ai/schema-update
realmarcin Dec 4, 2025
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .github/workflows/deploy_documentation.yml
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ jobs:
#----------------------------------------------
- name: Install dependencies
# if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
run: poetry install --no-interaction
run: poetry install --no-interaction --no-root

#----------------------------------------------
# Create documentation and deploy.
Expand Down
27 changes: 14 additions & 13 deletions .github/workflows/main.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -12,36 +12,37 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.9"]
python-version: ["3.12"]

steps:

#----------------------------------------------
# check-out repo and set-up python
#----------------------------------------------
- name: Check out repository
uses: actions/checkout@v2
uses: actions/checkout@v4

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

#----------------------------------------------
# install & configure poetry
# install & configure poetry via pip
#----------------------------------------------
- name: Install Poetry
uses: snok/[email protected]
with:
virtualenvs-create: true
virtualenvs-in-project: true
run: |
python -m pip install --upgrade pip
pip install poetry
poetry config virtualenvs.create true
poetry config virtualenvs.in-project true

#----------------------------------------------
# load cached venv if cache exists
# load cached venv if cache exists
#----------------------------------------------
- name: Load cached venv
id: cached-poetry-dependencies
uses: actions/cache@v2
uses: actions/cache@v4
with:
path: .venv
key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
Expand All @@ -54,10 +55,10 @@ jobs:
run: poetry install --no-interaction --no-root

#----------------------------------------------
# install your root project, if required
#----------------------------------------------
# install your root project, if required
#----------------------------------------------
- name: Install library
run: poetry install --no-interaction
run: poetry install --no-interaction --no-root

#----------------------------------------------
# run test suite
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/pypi-publish.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ jobs:
virtualenvs-in-project: true

- name: Install dependencies
run: poetry install --no-interaction
run: poetry install --no-interaction --no-root

- name: Build source and wheel archives
run: |
Expand Down
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -129,3 +129,4 @@ dmypy.json

# Pyre type checker
.pyre/
.DS_Store
Loading