From 8bc2ce6dddd06360ff220557447883b4d610cc90 Mon Sep 17 00:00:00 2001 From: Tao Liu Date: Tue, 20 Feb 2024 21:25:47 -0500 Subject: [PATCH 1/8] update docs 3.0.1 --- ChangeLog | 21 +++++++++---- README.md | 63 +++++++++++++++++++++++---------------- _config.yml | 5 ---- _layouts/default.html | 69 ------------------------------------------- conda/macs3/meta.yaml | 15 ++++++---- docs/source/index.md | 63 +++++++++++++++++++++++---------------- 6 files changed, 99 insertions(+), 137 deletions(-) delete mode 100644 _config.yml delete mode 100644 _layouts/default.html diff --git a/ChangeLog b/ChangeLog index 9cb17ff6..ffc60957 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,4 +1,4 @@ -2024-02-16 Tao Liu +2024-02-19 Tao Liu MACS 3.0.1 * Bugs fixed @@ -18,11 +18,21 @@ 'jaccard.py' to compute the Jaccard Index of two peak files. If the JI > 0.99 we would think the peaks called and the standard peaks are similar. This is to avoid the problem caused by - different Numpy libraries, when the certain peak coordinates may - have 1bp difference. + different Numpy/SciPy/sci-kit learn libraries, when certain peak + coordinates may have 10bps difference. #619 + + 4) Due to the changes in scikit-learn 1.3.0: + https://scikit-learn.org/1.3/whats_new/v1.3.html: The way hmmlearn + 0.3 uses Kmeans will end up with inconsistent results between + sklearn <1.3 and sklearn >=1.3. Therefore, we patched the class + hmm.GaussianHMM and adjusted the standard output from `hmmratac` + subcommand. The change is based on + https://github.com/hmmlearn/hmmlearn/pull/545. The idea is to do + the random seeding of KMeans 10 times. Now the `hmmratac` results + should be more consistent (at least JI>0.99). #615 #620 * Other - + 1) We added some dependencies to MACS3. `hmmratc` subcommand needs `hmmlearn` library, `hmmlearn` needs `scikit-learn` and `scikit-learn` needs `scipy`. Since major releases have happened @@ -30,7 +40,8 @@ version requirements for them in order to make sure the output results from `hmmratac` are consistent. - 2) We updated our documentation website using Sphinx. + 2) We updated our documentation website using + Sphinx. https://macs3-project.github.io/MACS/ 2023-11-15 Tao Liu MACS 3.0.0 diff --git a/README.md b/README.md index eaaf1b7b..740b7c17 100644 --- a/README.md +++ b/README.md @@ -27,38 +27,49 @@ applied to any "DNA enrichment assays" if the question to be asked is simply: *where we can find significant reads coverage than the random background*. -## Changes for MACS (3.0.1) +## Changes for MACS (3.0.1) *Bugs fixed* -1) Fixed a bug that the `hmmatac` can't correctly save the - digested signal files. #605 #611 - -2) Applied a patch to remove cython requirement from the installed - system. (it's needed for building the package). #606 #612 - -3) Relax the testing script while comparing the peaks called from - current codes and the standard peaks. #615. To implement this, we - added 'intersection' function to 'Regions' class to find the - intersecting regions of two Regions object (similar to PeakIO but - only recording chromosome, start and end positions). And we - updated the unit test 'test_Region.py' then implemented a script - 'jaccard.py' to compute the Jaccard Index of two peak files. If - the JI > 0.99 we would think the peaks called and the standard - peaks are similar. This is to avoid the problem caused by - different Numpy libraries, when the certain peak coordinates may - have 1bp difference. +1) Fixed a bug that the `hmmatac` can't correctly save the + digested signal files. #605 #611 + +2) Applied a patch to remove cython requirement from the installed + system. (it's needed for building the package). #606 #612 + +3) Relax the testing script while comparing the peaks called from + current codes and the standard peaks. #615. To implement this, we + added 'intersection' function to 'Regions' class to find the + intersecting regions of two Regions object (similar to PeakIO but + only recording chromosome, start and end positions). And we + updated the unit test 'test_Region.py' then implemented a script + 'jaccard.py' to compute the Jaccard Index of two peak files. If + the JI > 0.99 we would think the peaks called and the standard + peaks are similar. This is to avoid the problem caused by + different Numpy/SciPy/sci-kit learn libraries, when certain peak + coordinates may have 10bps difference. #619 + +4) Due to the changes in scikit-learn 1.3.0: + https://scikit-learn.org/1.3/whats_new/v1.3.html: The way hmmlearn + 0.3 uses Kmeans will end up with inconsistent results between + sklearn <1.3 and sklearn >=1.3. Therefore, we patched the class + hmm.GaussianHMM and adjusted the standard output from `hmmratac` + subcommand. The change is based on + https://github.com/hmmlearn/hmmlearn/pull/545. The idea is to do + the random seeding of KMeans 10 times. Now the `hmmratac` results + should be more consistent (at least JI>0.99). #615 #620 *Other* -1) We added some dependencies to MACS3. `hmmratc` subcommand needs - `hmmlearn` library, `hmmlearn` needs `scikit-learn` and - `scikit-learn` needs `scipy`. Since major releases have happened - for both`scipy` and `scikit-learn`, we have to set specific - version requirements for them in order to make sure the output - results from `hmmratac` are consistent. - -2) We updated our documentation website using Sphinx. +1) We added some dependencies to MACS3. `hmmratc` subcommand needs + `hmmlearn` library, `hmmlearn` needs `scikit-learn` and + `scikit-learn` needs `scipy`. Since major releases have happened + for both`scipy` and `scikit-learn`, we have to set specific + version requirements for them in order to make sure the output + results from `hmmratac` are consistent. + +2) We updated our documentation website using + Sphinx. https://macs3-project.github.io/MACS/ ## Changes for MACS (3.0.0) diff --git a/_config.yml b/_config.yml deleted file mode 100644 index f61fedf4..00000000 --- a/_config.yml +++ /dev/null @@ -1,5 +0,0 @@ -theme: jekyll-theme-slate -mathjax: - enable: true - combine: false - tags: "ams" \ No newline at end of file diff --git a/_layouts/default.html b/_layouts/default.html deleted file mode 100644 index 95932f06..00000000 --- a/_layouts/default.html +++ /dev/null @@ -1,69 +0,0 @@ - - - - - - - - - - - - - - - {% seo %} - {% include head-custom.html %} - - - - - -
-
- {% if site.github.is_project_page %} - View on GitHub - {% endif %} - -

{{ site.title | default: site.github.repository_name }}

-

{{ site.description | default: site.github.project_tagline }}

- - {% if site.show_downloads %} -
- Download this project as a .zip file - Download this project as a tar.gz file -
- {% endif %} -
-
- - -
-
- {{ content }} -
-
- - - - - \ No newline at end of file diff --git a/conda/macs3/meta.yaml b/conda/macs3/meta.yaml index dde98623..bfb3e012 100644 --- a/conda/macs3/meta.yaml +++ b/conda/macs3/meta.yaml @@ -18,23 +18,26 @@ requirements: - {{ compiler('c') }} - python >=3.11 - numpy >=1.25 - - scipy>=1.10 + - scipy >=1.12 - Cython ~=3.0 - - cykhash >=2.0 + - cykhash >=2.0,<3.0 - setuptools >=68.0 - hmmlearn >=0.3 - scikit-learn >=1.3 host: - python >=3.11 - numpy >=1.25 - - scipy>=1.10 - - Cython ~=3.0 - - cykhash >=2.0 + - scipy >=1.12 + - hmmlearn >=0.3 + - scikit-learn >=1.3 + - cykhash >=2.0,<3.0 run: - python >=3.11 - numpy >=1.25 - - scipy>=1.10 + - scipy >=1.12 - hmmlearn >=0.3 + - scikit-learn >=1.3 + - cykhash >=2.0,<3.0 test: commands: diff --git a/docs/source/index.md b/docs/source/index.md index e35d5f97..6e0c2e4e 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -27,38 +27,49 @@ applied to any "DNA enrichment assays" if the question to be asked is simply: *where we can find significant reads coverage than the random background*. -## Changes for MACS (3.0.1) +## Changes for MACS (3.0.1) *Bugs fixed* -1) Fixed a bug that the `hmmatac` can't correctly save the - digested signal files. #605 #611 - -2) Applied a patch to remove cython requirement from the installed - system. (it's needed for building the package). #606 #612 - -3) Relax the testing script while comparing the peaks called from - current codes and the standard peaks. #615. To implement this, we - added 'intersection' function to 'Regions' class to find the - intersecting regions of two Regions object (similar to PeakIO but - only recording chromosome, start and end positions). And we - updated the unit test 'test_Region.py' then implemented a script - 'jaccard.py' to compute the Jaccard Index of two peak files. If - the JI > 0.99 we would think the peaks called and the standard - peaks are similar. This is to avoid the problem caused by - different Numpy libraries, when the certain peak coordinates may - have 1bp difference. +1) Fixed a bug that the `hmmatac` can't correctly save the + digested signal files. #605 #611 + +2) Applied a patch to remove cython requirement from the installed + system. (it's needed for building the package). #606 #612 + +3) Relax the testing script while comparing the peaks called from + current codes and the standard peaks. #615. To implement this, we + added 'intersection' function to 'Regions' class to find the + intersecting regions of two Regions object (similar to PeakIO but + only recording chromosome, start and end positions). And we + updated the unit test 'test_Region.py' then implemented a script + 'jaccard.py' to compute the Jaccard Index of two peak files. If + the JI > 0.99 we would think the peaks called and the standard + peaks are similar. This is to avoid the problem caused by + different Numpy/SciPy/sci-kit learn libraries, when certain peak + coordinates may have 10bps difference. #619 + +4) Due to the changes in scikit-learn 1.3.0: + https://scikit-learn.org/1.3/whats_new/v1.3.html: The way hmmlearn + 0.3 uses Kmeans will end up with inconsistent results between + sklearn <1.3 and sklearn >=1.3. Therefore, we patched the class + hmm.GaussianHMM and adjusted the standard output from `hmmratac` + subcommand. The change is based on + https://github.com/hmmlearn/hmmlearn/pull/545. The idea is to do + the random seeding of KMeans 10 times. Now the `hmmratac` results + should be more consistent (at least JI>0.99). #615 #620 *Other* -1) We added some dependencies to MACS3. `hmmratc` subcommand needs - `hmmlearn` library, `hmmlearn` needs `scikit-learn` and - `scikit-learn` needs `scipy`. Since major releases have happened - for both`scipy` and `scikit-learn`, we have to set specific - version requirements for them in order to make sure the output - results from `hmmratac` are consistent. - -2) We updated our documentation website using Sphinx. +1) We added some dependencies to MACS3. `hmmratc` subcommand needs + `hmmlearn` library, `hmmlearn` needs `scikit-learn` and + `scikit-learn` needs `scipy`. Since major releases have happened + for both`scipy` and `scikit-learn`, we have to set specific + version requirements for them in order to make sure the output + results from `hmmratac` are consistent. + +2) We updated our documentation website using + Sphinx. https://macs3-project.github.io/MACS/ ## Changes for MACS (3.0.0) From 90b0a801293ea61f74ca2386856bbd34f93ac327 Mon Sep 17 00:00:00 2001 From: Tao Liu Date: Wed, 21 Feb 2024 10:43:06 -0500 Subject: [PATCH 2/8] update docs --- ChangeLog | 6 ++--- README.md | 60 +++++++++++++++++++++++++------------------- docs/source/index.md | 60 +++++++++++++++++++++++++------------------- make_docker_base.sh | 33 ------------------------ 4 files changed, 71 insertions(+), 88 deletions(-) delete mode 100644 make_docker_base.sh diff --git a/ChangeLog b/ChangeLog index ffc60957..99f718c2 100644 --- a/ChangeLog +++ b/ChangeLog @@ -10,8 +10,8 @@ system. (it's needed for building the package). #606 #612 3) Relax the testing script while comparing the peaks called from - current codes and the standard peaks. #615. To implement this, we - added 'intersection' function to 'Regions' class to find the + current codes and the standard peaks. To implement this, we added + 'intersection' function to 'Regions' class to find the intersecting regions of two Regions object (similar to PeakIO but only recording chromosome, start and end positions). And we updated the unit test 'test_Region.py' then implemented a script @@ -19,7 +19,7 @@ the JI > 0.99 we would think the peaks called and the standard peaks are similar. This is to avoid the problem caused by different Numpy/SciPy/sci-kit learn libraries, when certain peak - coordinates may have 10bps difference. #619 + coordinates may have 10bps difference. #615 #619 4) Due to the changes in scikit-learn 1.3.0: https://scikit-learn.org/1.3/whats_new/v1.3.html: The way hmmlearn diff --git a/README.md b/README.md index 740b7c17..9c4229d0 100644 --- a/README.md +++ b/README.md @@ -31,33 +31,41 @@ background*. *Bugs fixed* -1) Fixed a bug that the `hmmatac` can't correctly save the - digested signal files. #605 #611 - -2) Applied a patch to remove cython requirement from the installed - system. (it's needed for building the package). #606 #612 - -3) Relax the testing script while comparing the peaks called from - current codes and the standard peaks. #615. To implement this, we - added 'intersection' function to 'Regions' class to find the - intersecting regions of two Regions object (similar to PeakIO but - only recording chromosome, start and end positions). And we - updated the unit test 'test_Region.py' then implemented a script - 'jaccard.py' to compute the Jaccard Index of two peak files. If - the JI > 0.99 we would think the peaks called and the standard - peaks are similar. This is to avoid the problem caused by - different Numpy/SciPy/sci-kit learn libraries, when certain peak - coordinates may have 10bps difference. #619 +1) Fixed a bug that the `hmmatac` can't correctly save the digested + signal + files. [#605](https://github.com/macs3-project/MACS/issues/605) + [#611](https://github.com/macs3-project/MACS/pull/611) + +2) Applied a patch to remove cython requirement from the installed + system. (it's needed for building the + package). [#606](https://github.com/macs3-project/MACS/issues/606) + [#612](https://github.com/macs3-project/MACS/pull/612) + +3) Relax the testing script while comparing the peaks called from + current codes and the standard peaks. To implement this, we added + 'intersection' function to 'Regions' class to find the + intersecting regions of two Regions object (similar to PeakIO but + only recording chromosome, start and end positions). And we + updated the unit test 'test_Region.py' then implemented a script + 'jaccard.py' to compute the Jaccard Index of two peak files. If + the JI > 0.99 we would think the peaks called and the standard + peaks are similar. This is to avoid the problem caused by + different Numpy/SciPy/sci-kit learn libraries, when certain peak + coordinates may have 10bps + difference. [#615](https://github.com/macs3-project/MACS/issues/615) + [#619](https://github.com/macs3-project/MACS/pull/619) -4) Due to the changes in scikit-learn 1.3.0: - https://scikit-learn.org/1.3/whats_new/v1.3.html: The way hmmlearn - 0.3 uses Kmeans will end up with inconsistent results between - sklearn <1.3 and sklearn >=1.3. Therefore, we patched the class - hmm.GaussianHMM and adjusted the standard output from `hmmratac` - subcommand. The change is based on - https://github.com/hmmlearn/hmmlearn/pull/545. The idea is to do - the random seeding of KMeans 10 times. Now the `hmmratac` results - should be more consistent (at least JI>0.99). #615 #620 +4) Due to [the changes in scikit-learn + 1.3.0](https://scikit-learn.org/1.3/whats_new/v1.3.html), the way + hmmlearn 0.3 uses Kmeans will end up with inconsistent results + between sklearn <1.3 and sklearn >=1.3. Therefore, we patched the + class hmm.GaussianHMM and adjusted the standard output from + `hmmratac` subcommand. The change is based on [hmmlearn + PR#545](https://github.com/hmmlearn/hmmlearn/pull/545). The idea + is to do the random seeding of KMeans 10 times. Now the `hmmratac` + results should be more consistent (at least + JI>0.99). [#615](https://github.com/macs3-project/MACS/issues/615) + [#620](https://github.com/macs3-project/MACS/pull/620) *Other* diff --git a/docs/source/index.md b/docs/source/index.md index 6e0c2e4e..5dc50eb0 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -31,33 +31,41 @@ background*. *Bugs fixed* -1) Fixed a bug that the `hmmatac` can't correctly save the - digested signal files. #605 #611 - -2) Applied a patch to remove cython requirement from the installed - system. (it's needed for building the package). #606 #612 - -3) Relax the testing script while comparing the peaks called from - current codes and the standard peaks. #615. To implement this, we - added 'intersection' function to 'Regions' class to find the - intersecting regions of two Regions object (similar to PeakIO but - only recording chromosome, start and end positions). And we - updated the unit test 'test_Region.py' then implemented a script - 'jaccard.py' to compute the Jaccard Index of two peak files. If - the JI > 0.99 we would think the peaks called and the standard - peaks are similar. This is to avoid the problem caused by - different Numpy/SciPy/sci-kit learn libraries, when certain peak - coordinates may have 10bps difference. #619 +1) Fixed a bug that the `hmmatac` can't correctly save the digested + signal + files. [#605](https://github.com/macs3-project/MACS/issues/605) + [#611](https://github.com/macs3-project/MACS/pull/611) + +2) Applied a patch to remove cython requirement from the installed + system. (it's needed for building the + package). [#606](https://github.com/macs3-project/MACS/issues/606) + [#612](https://github.com/macs3-project/MACS/pull/612) + +3) Relax the testing script while comparing the peaks called from + current codes and the standard peaks. To implement this, we added + 'intersection' function to 'Regions' class to find the + intersecting regions of two Regions object (similar to PeakIO but + only recording chromosome, start and end positions). And we + updated the unit test 'test_Region.py' then implemented a script + 'jaccard.py' to compute the Jaccard Index of two peak files. If + the JI > 0.99 we would think the peaks called and the standard + peaks are similar. This is to avoid the problem caused by + different Numpy/SciPy/sci-kit learn libraries, when certain peak + coordinates may have 10bps + difference. [#615](https://github.com/macs3-project/MACS/issues/615) + [#619](https://github.com/macs3-project/MACS/pull/619) -4) Due to the changes in scikit-learn 1.3.0: - https://scikit-learn.org/1.3/whats_new/v1.3.html: The way hmmlearn - 0.3 uses Kmeans will end up with inconsistent results between - sklearn <1.3 and sklearn >=1.3. Therefore, we patched the class - hmm.GaussianHMM and adjusted the standard output from `hmmratac` - subcommand. The change is based on - https://github.com/hmmlearn/hmmlearn/pull/545. The idea is to do - the random seeding of KMeans 10 times. Now the `hmmratac` results - should be more consistent (at least JI>0.99). #615 #620 +4) Due to [the changes in scikit-learn + 1.3.0](https://scikit-learn.org/1.3/whats_new/v1.3.html), the way + hmmlearn 0.3 uses Kmeans will end up with inconsistent results + between sklearn <1.3 and sklearn >=1.3. Therefore, we patched the + class hmm.GaussianHMM and adjusted the standard output from + `hmmratac` subcommand. The change is based on [hmmlearn + PR#545](https://github.com/hmmlearn/hmmlearn/pull/545). The idea + is to do the random seeding of KMeans 10 times. Now the `hmmratac` + results should be more consistent (at least + JI>0.99). [#615](https://github.com/macs3-project/MACS/issues/615) + [#620](https://github.com/macs3-project/MACS/pull/620) *Other* diff --git a/make_docker_base.sh b/make_docker_base.sh deleted file mode 100644 index eb171e1f..00000000 --- a/make_docker_base.sh +++ /dev/null @@ -1,33 +0,0 @@ -# This script contains commands to create docker images for multi-arch -# testing of MACS3. Note that The dependencies to compile and run -# MACS3 have been installed in these images; however, MACS3 is not -# installed. After creating the images, one can `docker run` a -# container while mounting the MACS source code directory, then -# compile/install MACS and run `pytest` and `cmdlinetest`. -# -# e.g. -# $ docker run --rm -it -v $PWD:/macs3_codes -t macs_ppc64le_base - -# base images are from Debian official images - -# create Docker image for testing MACS3 in ppc64le -docker run --rm --privileged multiarch/qemu-user-static --reset -p yes && - docker build --rm --build-arg BASE_IMAGE="ppc64le/debian:buster" -t macs_ppc64le_base -f test/Dockerfile.multiarch.base.buster.py37 . - -# create Docker image for testing MACS3 in i386 -docker run --rm --privileged multiarch/qemu-user-static --reset -p yes && - docker build --rm --build-arg BASE_IMAGE="i386/debian:buster" -t macs_i386_base -f test/Dockerfile.multiarch.base.buster.py37 . - -# create Docker image for testing MACS3 in arm32v7 -docker run --rm --privileged multiarch/qemu-user-static --reset -p yes && - docker build --rm --build-arg BASE_IMAGE="arm32v7/debian:buster" -t macs_arm32v7_base -f test/Dockerfile.multiarch.base.buster.py37 . - -# create Docker image for testing MACS3 in arm64v8/aarch64 -docker run --rm --privileged multiarch/qemu-user-static --reset -p yes && - docker build --rm --build-arg BASE_IMAGE="arm64v8/debian:buster" -t macs_arm64v8_base -f test/Dockerfile.multiarch.base.buster.py37 . - -# create Docker image for testing MACS3 in s390x -docker run --rm --privileged multiarch/qemu-user-static --reset -p yes && - docker build --rm --build-arg BASE_IMAGE="s390x/debian:buster" -t macs_s390x_base -f test/Dockerfile.multiarch.base.buster.py37 . - -# The final images are macs_ppc64le_base, macs_i386_base, macs_arm32v7_base, macs_arm64v8_base, and macs_s390x_base From 6ee80836bbaec61a714249586c321d892105d374 Mon Sep 17 00:00:00 2001 From: Tao Liu Date: Thu, 22 Feb 2024 00:33:25 -0500 Subject: [PATCH 3/8] for conda build, add Cython to host section --- conda/macs3/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/conda/macs3/meta.yaml b/conda/macs3/meta.yaml index bfb3e012..1efabe11 100644 --- a/conda/macs3/meta.yaml +++ b/conda/macs3/meta.yaml @@ -28,6 +28,7 @@ requirements: - python >=3.11 - numpy >=1.25 - scipy >=1.12 + - Cython ~=3.0 - hmmlearn >=0.3 - scikit-learn >=1.3 - cykhash >=2.0,<3.0 From d68d6b268693682244aa8da19158baa419eee7e8 Mon Sep 17 00:00:00 2001 From: Tao Liu Date: Thu, 22 Feb 2024 01:26:41 -0500 Subject: [PATCH 4/8] for conda build, add zlib --- conda/macs3/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/conda/macs3/meta.yaml b/conda/macs3/meta.yaml index 1efabe11..a88491ca 100644 --- a/conda/macs3/meta.yaml +++ b/conda/macs3/meta.yaml @@ -16,6 +16,7 @@ build: requirements: build: - {{ compiler('c') }} + - zlib - python >=3.11 - numpy >=1.25 - scipy >=1.12 @@ -26,6 +27,7 @@ requirements: - scikit-learn >=1.3 host: - python >=3.11 + - zlib - numpy >=1.25 - scipy >=1.12 - Cython ~=3.0 From b1fff6a35f3fb9dd9c8d56f72fa35e853fa65e5c Mon Sep 17 00:00:00 2001 From: Tao Liu Date: Thu, 22 Feb 2024 01:50:46 -0500 Subject: [PATCH 5/8] for conda build, only do pytest --- conda/macs3/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/conda/macs3/meta.yaml b/conda/macs3/meta.yaml index a88491ca..7711730a 100644 --- a/conda/macs3/meta.yaml +++ b/conda/macs3/meta.yaml @@ -44,7 +44,6 @@ requirements: test: commands: - - macs3 -h - pytest about: From a9a7e6b17bfe45b9f185c7115df7c61fd6fed28b Mon Sep 17 00:00:00 2001 From: Tao Liu Date: Thu, 22 Feb 2024 01:58:27 -0500 Subject: [PATCH 6/8] for conda build, no test --- conda/macs3/meta.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/conda/macs3/meta.yaml b/conda/macs3/meta.yaml index 7711730a..a29d3b72 100644 --- a/conda/macs3/meta.yaml +++ b/conda/macs3/meta.yaml @@ -42,10 +42,6 @@ requirements: - scikit-learn >=1.3 - cykhash >=2.0,<3.0 -test: - commands: - - pytest - about: home: http://github.com/macs3-project/MACS/ license: BSD From 67e4a4a6fefddf13555155ef7e6f8b0832223d46 Mon Sep 17 00:00:00 2001 From: Tao Liu Date: Thu, 22 Feb 2024 19:44:51 -0500 Subject: [PATCH 7/8] after conda build, add pytest through conda --- .github/workflows/publish-to-anaconda.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/publish-to-anaconda.yml b/.github/workflows/publish-to-anaconda.yml index 8c37fce8..48477be4 100644 --- a/.github/workflows/publish-to-anaconda.yml +++ b/.github/workflows/publish-to-anaconda.yml @@ -62,6 +62,7 @@ jobs: run: | source /usr/share/miniconda/etc/profile.d/conda.sh conda activate MACS3 + conda install -q pytest pytest --runxfail cd test ./cmdlinetest macs3 From 08b860844296fa7b8bf8cb22845b7660469c9c5d Mon Sep 17 00:00:00 2001 From: Tao Liu Date: Fri, 23 Feb 2024 00:43:07 -0500 Subject: [PATCH 8/8] update conda badge --- README.md | 1 + docs/source/index.md | 1 + 2 files changed, 2 insertions(+) diff --git a/README.md b/README.md index 9c4229d0..39e7a698 100644 --- a/README.md +++ b/README.md @@ -8,6 +8,7 @@ download](https://img.shields.io/pypi/dm/macs3?label=pypi%20downloads)](https:// Latest Release: * Github: [![Github Release](https://img.shields.io/github/v/release/macs3-project/MACS)](https://github.com/macs3-project/MACS/releases) * PyPI: [![PyPI Release](https://img.shields.io/pypi/v/macs3.svg) ![PyPI Python Version](https://img.shields.io/pypi/pyversions/MACS3) ![PyPI Format](https://img.shields.io/pypi/format/macs3)](https://pypi.org/project/macs3/) +* Anaconda:[![Anaconda-Server Badge](https://anaconda.org/macs3/macs3/badges/version.svg)](https://anaconda.org/macs3/macs3) ## Introduction diff --git a/docs/source/index.md b/docs/source/index.md index 5dc50eb0..1b369cf4 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -8,6 +8,7 @@ download](https://img.shields.io/pypi/dm/macs3?label=pypi%20downloads)](https:// Latest Release: * Github: [![Github Release](https://img.shields.io/github/v/release/macs3-project/MACS)](https://github.com/macs3-project/MACS/releases) * PyPI: [![PyPI Release](https://img.shields.io/pypi/v/macs3.svg) ![PyPI Python Version](https://img.shields.io/pypi/pyversions/MACS3) ![PyPI Format](https://img.shields.io/pypi/format/macs3)](https://pypi.org/project/macs3/) +* Anaconda:[![Anaconda-Server Badge](https://anaconda.org/macs3/macs3/badges/version.svg)](https://anaconda.org/macs3/macs3) ## Introduction