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171fac3
downgrading pandas and numpy for compatibility with callingcardstools
cmatKhan May 6, 2025
e59fdb2
Merge pull request #8 from cmatKhan/degrade_pandas_numpy
cmatKhan May 6, 2025
6f94ad0
adding umapi
cmatKhan May 6, 2025
544cf66
Merge pull request #9 from cmatKhan/add_univariatemodelsapi
cmatKhan May 6, 2025
c049868
updating init to include umapi
cmatKhan May 6, 2025
f55853d
Merge branch 'dev' of https://github.com/BrentLab/tfbpapi into dev
cmatKhan May 6, 2025
468152a
removing yeastdnnexplorer from import
cmatKhan May 6, 2025
d11f77e
adding dotenv to deps
cmatKhan Jul 10, 2025
669c2f0
Merge pull request #15 from cmatKhan/dev
cmatKhan Jul 10, 2025
f58ff0c
adding filter params and updating numpy and pandas
cmatKhan Sep 5, 2025
a7ced03
Merge pull request #24 from cmatKhan/add_params
cmatKhan Sep 8, 2025
ca24fb4
resolving requests missing types
cmatKhan Sep 8, 2025
c75f6d3
adding tests for AbstractHfAPI
cmatKhan Sep 8, 2025
c8e0c39
removing windows-2019 from ci
cmatKhan Sep 8, 2025
c164f32
working on adding rank response functionality
cmatKhan Sep 10, 2025
0494d09
this is getting closer to what im after. datainfo is close to finishe…
cmatKhan Sep 18, 2025
fff878d
this is getting closer to what im after. datainfo is close to finishe…
cmatKhan Sep 18, 2025
cad9834
working on hfqueryapi
cmatKhan Sep 20, 2025
1dd92d4
adding rank response tutorial and role to features
cmatKhan Sep 25, 2025
db7dd01
correlation analysis tutorial draft
CalvinFang-code Oct 10, 2025
87a9ad1
kaiwens correlation tutorial
cmatKhan Oct 15, 2025
921f49a
Merge pull request #37 from cmatKhan/correlation_tutorial
cmatKhan Oct 15, 2025
2faf66d
documenting factor levels of experimental condition features
cmatKhan Dec 3, 2025
dc56e3f
documenting factor levels of experimental condition features
cmatKhan Dec 3, 2025
ebf74a6
adding metadata_manager
cmatKhan Dec 9, 2025
1deb529
rendered metadata explorer notebook
cmatKhan Dec 9, 2025
ce67e2c
continuing to refine metadata manager
cmatKhan Dec 9, 2025
3f2b04e
revising how cond cols are displayed
cmatKhan Dec 9, 2025
8005ad2
tmp
cmatKhan Dec 11, 2025
26c686b
filter_resolver
cmatKhan Dec 11, 2025
10e042c
intermediate
cmatKhan Dec 15, 2025
1d7da51
tmp
cmatKhan Dec 16, 2025
d73a82a
tmp
cmatKhan Dec 16, 2025
a51fa91
tmp
cmatKhan Dec 16, 2025
9608f57
tmp
cmatKhan Dec 18, 2025
990f81f
tmp
cmatKhan Dec 18, 2025
d33274e
tfbpapi virtual_db is working
cmatKhan Jan 7, 2026
e71f804
resolving requests missing types
cmatKhan Sep 8, 2025
188e276
adding tests for AbstractHfAPI
cmatKhan Sep 8, 2025
e7fb52e
removing windows-2019 from ci
cmatKhan Sep 8, 2025
177d245
working on adding rank response functionality
cmatKhan Sep 10, 2025
74b4f8c
this is getting closer to what im after. datainfo is close to finishe…
cmatKhan Sep 18, 2025
594eb6f
this is getting closer to what im after. datainfo is close to finishe…
cmatKhan Sep 18, 2025
ac55a4b
working on hfqueryapi
cmatKhan Sep 20, 2025
057742e
adding rank response tutorial and role to features
cmatKhan Sep 25, 2025
e10ec2c
kaiwens correlation tutorial
cmatKhan Oct 15, 2025
94cfd21
documenting factor levels of experimental condition features
cmatKhan Dec 3, 2025
1608bdf
documenting factor levels of experimental condition features
cmatKhan Dec 3, 2025
2d817ea
adding metadata_manager
cmatKhan Dec 9, 2025
3ce7c81
rendered metadata explorer notebook
cmatKhan Dec 9, 2025
7c8eb72
continuing to refine metadata manager
cmatKhan Dec 9, 2025
235dc50
revising how cond cols are displayed
cmatKhan Dec 9, 2025
cb165e7
tmp
cmatKhan Dec 11, 2025
e894cde
filter_resolver
cmatKhan Dec 11, 2025
a552349
intermediate
cmatKhan Dec 15, 2025
ea90de0
tmp
cmatKhan Dec 16, 2025
38e0b91
tmp
cmatKhan Dec 16, 2025
e91565b
tmp
cmatKhan Dec 16, 2025
e3422e5
tmp
cmatKhan Dec 18, 2025
b1fcb1f
tmp
cmatKhan Dec 18, 2025
ab02d28
tfbpapi virtual_db is working
cmatKhan Jan 7, 2026
abcdd3c
Merge branch 'update_docs_expr_conds' of https://github.com/cmatKhan/…
cmatKhan Jan 7, 2026
3762ed3
Merge pull request #52 from cmatKhan/update_docs_expr_conds
cmatKhan Jan 7, 2026
ed93eee
updating mac os runner
cmatKhan Jan 7, 2026
60e5c4a
addressing precommit failures
cmatKhan Jan 7, 2026
6a52cc6
addressing precommit
cmatKhan Jan 7, 2026
da8a92a
addressing precommit
cmatKhan Jan 7, 2026
e3636e9
addressing precommit
cmatKhan Jan 7, 2026
cfd743b
addressing precommit
cmatKhan Jan 7, 2026
c2ec729
Merge pull request #54 from BrentLab/huggingface
cmatKhan Jan 7, 2026
5675a52
this includes refinements of the models.py module, and a generalizati…
cmatKhan Feb 4, 2026
8e1e754
major update to virtualdb interface
cmatKhan Feb 6, 2026
2724b59
Merge pull request #73 from cmatKhan/huggingface
cmatKhan Feb 6, 2026
809594a
cleaning up docs
cmatKhan Feb 6, 2026
21f6511
Merge pull request #74 from cmatKhan/touch_up_docs
cmatKhan Feb 6, 2026
8939ee0
this seems to work
cmatKhan Feb 18, 2026
f00c15a
Update tfbpapi/datacard.py
cmatKhan Feb 18, 2026
b06aed9
adding documentation on calling _db directly from virtual_db
cmatKhan Mar 4, 2026
cb4cbba
adding tags
cmatKhan Mar 4, 2026
3cb8cf7
updating tutorial with tags
cmatKhan Mar 4, 2026
ee655ad
Merge pull request #79 from cmatKhan/dealing_with_nonembedded
cmatKhan Mar 4, 2026
837b46c
adding get_datasets method to virtualdb
cmatKhan Mar 4, 2026
2eba367
Merge pull request #82 from cmatKhan/add_get_datasets
cmatKhan Mar 4, 2026
55585b9
updates necessary for dto rr analysis
cmatKhan Mar 10, 2026
e8a3ac5
Merge pull request #83 from cmatKhan/dto_rr_analysis
cmatKhan Mar 10, 2026
a278c40
adding dtype factor and updating local branch of dev
cmatKhan Mar 11, 2026
f989b16
tryign to resovle merge conflicts
cmatKhan Mar 11, 2026
83c3382
removing duplicate code lines
cmatKhan Mar 11, 2026
385ee57
still removing duplicate lines
cmatKhan Mar 11, 2026
8f1a20f
Merge pull request #86 from cmatKhan/add_factor_option_vdbconfig
cmatKhan Mar 11, 2026
802176a
fixing nonembedded and dtype factor
cmatKhan Mar 11, 2026
7015f16
Merge pull request #88 from cmatKhan/fixing_nonembedded
cmatKhan Mar 11, 2026
44473d6
if missing_value_labels is specified, then any dataset without that s…
cmatKhan Mar 11, 2026
2d92fd8
Merge pull request #90 from cmatKhan/missing_value_labels_fix
cmatKhan Mar 11, 2026
d09670b
updating vdb tutorial rendering
cmatKhan Mar 12, 2026
5040b68
Merge pull request #91 from cmatKhan/updating_virtual_db_tutorial
cmatKhan Mar 12, 2026
0bf4af6
adding query error to query() when failed to print sql and params
cmatKhan Mar 13, 2026
e7e2cc0
Merge pull request #92 from cmatKhan/add_QueryError_class
cmatKhan Mar 13, 2026
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9 changes: 1 addition & 8 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -32,14 +32,7 @@ jobs:
strategy:
matrix:
# see https://github.com/actions/runner-images
os:
[
ubuntu-22.04,
ubuntu-24.04,
macos-13,
windows-2022,
windows-2019,
]
os: [ubuntu-22.04, ubuntu-24.04, macos-15, windows-2022]
python-version: ["3.11"]
runs-on: ${{ matrix.os }}
steps:
Expand Down
10 changes: 8 additions & 2 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,8 +1,14 @@
#mac files
# claude
CLAUDE.md
.claude/
claude_output/
claude_logs/

# mac files
**/.DS_Store

# Dataset directory
data/
./data/

# logs
**/logs/
Expand Down
3 changes: 2 additions & 1 deletion .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
exclude: ^docs/|devcontainer.json|.*/snapshots/
exclude: ^docs/|devcontainer.json|.*/snapshots/|mkdocs.yml
default_stages: [commit]

default_language_version:
Expand Down Expand Up @@ -62,6 +62,7 @@ repos:
rev: v1.15.0
hooks:
- id: mypy
additional_dependencies: [types-requests]

- repo: https://github.com/markdownlint/markdownlint
rev: v0.12.0
Expand Down
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