-
Notifications
You must be signed in to change notification settings - Fork 3.3k
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'master' into add_lodei
- Loading branch information
Showing
15 changed files
with
153 additions
and
54 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,22 +1,22 @@ | ||
| #!/usr/bin/env bash | ||
| #!/usr/bin/bash | ||
|
|
||
| set -o errexit | ||
| set -o nounset | ||
|
|
||
| if [ -e "$PREFIX/include" ]; then | ||
| export CPPFLAGS="${CPPFLAGS:+$CPPFLAGS }-I$PREFIX/include" | ||
| export CPPFLAGS="${CPPFLAGS:+$CPPFLAGS }-I${PREFIX}/include" | ||
| fi | ||
|
|
||
| if [ -e "$PREFIX/lib" ]; then | ||
| export LDFLAGS="${LDFLAGS:+$LDFLAGS }-L$PREFIX/lib" | ||
| export LDFLAGS="${LDFLAGS:+$LDFLAGS }-L${PREFIX}/lib" | ||
| fi | ||
|
|
||
| echo "CPPFLAGS=\"$CPPFLAGS\"" | ||
| echo "LDFLAGS=\"$LDFLAGS\"" | ||
|
|
||
| cd "$SRC_DIR" | ||
|
|
||
| make | ||
| make CXX="${CXX}" CPPFLAGS="${CPPFLAGS}" -j"${CPU_COUNT}" | ||
|
|
||
| install -d "$PREFIX/bin" | ||
| install -v -m 0755 build/bin/rdeval "$PREFIX/bin/" | ||
| install -v -m 0755 build/bin/rdeval "$PREFIX/bin" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| {% set name = "stripepy-hic" %} | ||
| {% set version = "0.0.2" %} | ||
| {% set sha256 = "4e0e14f365334095b9af04874b01bae25fb385560add5f6f0bc91b35f757e556" %} | ||
|
|
||
| package: | ||
| name: {{ name|lower }} | ||
| version: {{ version }} | ||
|
|
||
| source: | ||
| url: https://pypi.org/packages/source/{{ name[0] }}/{{ name|replace("-", "_") }}/{{ name|replace("-", "_") }}-{{ version }}.tar.gz | ||
| sha256: {{ sha256 }} | ||
|
|
||
| build: | ||
| number: 0 | ||
| noarch: python | ||
| entry_points: | ||
| - stripepy = stripepy:main | ||
| script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -v" | ||
| run_exports: | ||
| - {{ pin_subpackage('stripepy-hic', max_pin="x.x") }} | ||
|
|
||
| requirements: | ||
| host: | ||
| - python >=3.9 | ||
| - pip | ||
| - hatchling | ||
| - hatch-vcs | ||
| run: | ||
| - h5py >=3 | ||
| - hictkpy >=1 | ||
| - matplotlib-base >=3.8 | ||
| - numpy | ||
| - pandas >=2 | ||
| - scikit-learn | ||
| - scipy | ||
| - seaborn-base >=0.13 | ||
|
|
||
| about: | ||
| home: https://github.com/paulsengroup/StripePy | ||
| license: MIT | ||
| license_file: LICENCE | ||
| summary: "StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning" | ||
| dev_url: https://github.com/paulsengroup/StripePy | ||
| doc_url: https://github.com/paulsengroup/StripePy/blob/main/README.md | ||
|
|
||
| test: | ||
| requires: | ||
| - curl | ||
| - perl-digest-md5 | ||
| - pytest>=8 | ||
| source_files: | ||
| - test/* | ||
| imports: | ||
| - stripepy | ||
|
|
||
| extra: | ||
| recipe-maintainers: | ||
| - robomics | ||
| - rea1991 | ||
| - jonnings | ||
| identifiers: | ||
| - biotools:stripepy-hic | ||
| - doi:10.5281/zenodo.14394041 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| #!/usr/bin/env bash | ||
|
|
||
| # Download test datasets | ||
| mkdir -p test/data | ||
|
|
||
| curl -L 'https://zenodo.org/records/14517632/files/4DNFI9GMP2J8.stripepy.mcool?download=1' -o test/data/4DNFI9GMP2J8.mcool | ||
| curl -L 'https://zenodo.org/records/14517632/files/results_4DNFI9GMP2J8_v1.hdf5?download=1' -o test/data/results_4DNFI9GMP2J8_v1.hdf5 | ||
|
|
||
| # Checksum datasets | ||
| echo 'a17d08460c03cf6c926e2ca5743e4888 test/data/4DNFI9GMP2J8.mcool' > checksums.md5 | ||
| echo '632b2a7a6e5c1a24dc3635710ed68a80 test/data/results_4DNFI9GMP2J8_v1.hdf5' >> checksums.md5 | ||
|
|
||
| md5sum -c checksums.md5 | ||
|
|
||
| # Test CLI | ||
| stripepy --help | ||
| stripepy --version | ||
|
|
||
| # Run automated test suites | ||
| "$PYTHON" -m pytest test/ -m unit -v --disable-pytest-warnings | ||
| "$PYTHON" -m pytest test/ -m end2end -v -k 'not TestStripePyPlot' --disable-pytest-warnings |
Oops, something went wrong.