From c769f913e9e43666c5ff433cfbfaab5f6789c7e9 Mon Sep 17 00:00:00 2001 From: Dana-Farber Date: Fri, 16 Dec 2022 11:07:11 -0500 Subject: [PATCH 01/39] add users and papers to README --- README.md | 36 +++++++++++++++++++++++++++++++----- 1 file changed, 31 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 745e0fc2..4ec3a8ce 100644 --- a/README.md +++ b/README.md @@ -191,12 +191,38 @@ See [contributing](https://github.com/Dana-Farber-AIOS/pathml/blob/master/CONTRI # Citing -If you use `PathML` in your work, please cite our paper: +If you use `PathML` please cite: + +[**J. Rosenthal et al., "Building tools for machine learning and artificial intelligence in cancer research: best practices and a case study with the PathML toolkit for computational pathology." Molecular Cancer Research, 2022.**](https://doi.org/10.1158/1541-7786.MCR-21-0665) + +So far, PathML was used in the following manuscripts: + +- [A. Shmatko et al. **Nature Cancer** 2022](https://www.nature.com/articles/s43018-022-00436-4) +- [J. Pocock et al. **Nature Communications Medicine** 2022](https://www.nature.com/articles/s43856-022-00186-5) +- [A. Marcolini et al. **SoftwareX** 2022](https://www.sciencedirect.com/science/article/pii/S2352711022001558) +- [M. Rahman et al. **Bioengineering** 2022](https://www.mdpi.com/2306-5354/9/8/335) +- [C. Lama et al. **bioRxiv** 2022](https://www.biorxiv.org/content/10.1101/2022.09.28.509751v1.full) +- [D. Brundage et al. **arXiv** 2022](https://arxiv.org/abs/2203.13888) +- [S. Orsulic et al. **Frontiers in Oncology** 2022](https://www.frontiersin.org/articles/10.3389/fonc.2022.924945/full) +- [J. Linares et al. **Molecular Cell** 2021](https://www.cell.com/molecular-cell/fulltext/S1097-2765(21)00729-2) + +# Users + + + + +
+This is where in the world our most enthusiastic supporters are located: + + + +and this is where they work: + + +
+ +Source: https://ossinsight.io/analyze/Dana-Farber-AIOS/pathml#people -Rosenthal J, Carelli R, Omar M, Brundage D, Halbert E, Nyman J, Hari SN, Van Allen EM, Marchionni L, Umeton R, Loda M. -Building tools for machine learning and artificial intelligence in cancer research: best practices and a case study -with the PathML toolkit for computational pathology. *Molecular Cancer Research*, 2021. -DOI: [10.1158/1541-7786.MCR-21-0665](https://doi.org/10.1158/1541-7786.MCR-21-0665) # License From c71bc9bd5ffc652edd2ad143e5c4e31659db0598 Mon Sep 17 00:00:00 2001 From: Dana-Farber Date: Fri, 16 Dec 2022 11:25:35 -0500 Subject: [PATCH 02/39] Update README.md --- README.md | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 4ec3a8ce..de438714 100644 --- a/README.md +++ b/README.md @@ -193,7 +193,7 @@ See [contributing](https://github.com/Dana-Farber-AIOS/pathml/blob/master/CONTRI If you use `PathML` please cite: -[**J. Rosenthal et al., "Building tools for machine learning and artificial intelligence in cancer research: best practices and a case study with the PathML toolkit for computational pathology." Molecular Cancer Research, 2022.**](https://doi.org/10.1158/1541-7786.MCR-21-0665) +- [**J. Rosenthal et al., "Building tools for machine learning and artificial intelligence in cancer research: best practices and a case study with the PathML toolkit for computational pathology." Molecular Cancer Research, 2022.**](https://doi.org/10.1158/1541-7786.MCR-21-0665) So far, PathML was used in the following manuscripts: @@ -208,21 +208,18 @@ So far, PathML was used in the following manuscripts: # Users - -
-This is where in the world our most enthusiastic supporters are located: - +
This is where in the world our most enthusiastic supporters are located: +

and this is where they work: - +

- -Source: https://ossinsight.io/analyze/Dana-Farber-AIOS/pathml#people +Source: https://ossinsight.io/analyze/Dana-Farber-AIOS/pathml#people # License From c4a72ff43c6f89f3897783a1d68fed8147abae7d Mon Sep 17 00:00:00 2001 From: Dana-Farber Date: Tue, 7 Feb 2023 15:21:19 -0500 Subject: [PATCH 03/39] Update README.md --- README.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index de438714..16b97e8e 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,11 @@ +🤖đŸ”Ŧ **PathML: Tools for computational pathology.** + +⭐ **PathML objective is to lower the barrier to entry to digital pathology.** + +ℹī¸ Imaging datasets in cancer research are growing exponentially in both quantity and information density. These massive datasets may enable derivation of insights for cancer research and clinical care, but only if researchers are equipped with the tools to leverage advanced computational analysis approaches such as machine learning and artificial intelligence. In this work, we highlight three themes to guide development of such computational tools: scalability, standardization, and ease of use. We then apply these principles to develop PathML, a general-purpose research toolkit for computational pathology. We describe the design of the PathML framework and demonstrate applications in diverse use cases. + +🚀 The fastest way to get started? `docker pull pathml/pathml` + @@ -232,6 +240,6 @@ Commercial license options are available also. Questions? Comments? Suggestions? Get in touch! -[PathML@dfci.harvard.edu](mailto:PathML@dfci.harvard.edu) +[pathml@dfci.harvard.edu](mailto:pathml@dfci.harvard.edu) From 0d78e459b286ed928a054dd27318a8bfa5aec6ac Mon Sep 17 00:00:00 2001 From: Dana-Farber Date: Tue, 7 Feb 2023 19:25:09 -0500 Subject: [PATCH 04/39] Update README.md --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 16b97e8e..4bde3eb8 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ ℹī¸ Imaging datasets in cancer research are growing exponentially in both quantity and information density. These massive datasets may enable derivation of insights for cancer research and clinical care, but only if researchers are equipped with the tools to leverage advanced computational analysis approaches such as machine learning and artificial intelligence. In this work, we highlight three themes to guide development of such computational tools: scalability, standardization, and ease of use. We then apply these principles to develop PathML, a general-purpose research toolkit for computational pathology. We describe the design of the PathML framework and demonstrate applications in diverse use cases. -🚀 The fastest way to get started? `docker pull pathml/pathml` +🚀 The fastest way to get started? `docker pull pathml/pathml && docker run -it -p 8888:8888 pathml/pathml` @@ -205,14 +205,15 @@ If you use `PathML` please cite: So far, PathML was used in the following manuscripts: +- [J. Linares et al. **Molecular Cell** 2021](https://www.cell.com/molecular-cell/fulltext/S1097-2765(21)00729-2) - [A. Shmatko et al. **Nature Cancer** 2022](https://www.nature.com/articles/s43018-022-00436-4) - [J. Pocock et al. **Nature Communications Medicine** 2022](https://www.nature.com/articles/s43856-022-00186-5) +- [S. Orsulic et al. **Frontiers in Oncology** 2022](https://www.frontiersin.org/articles/10.3389/fonc.2022.924945/full) +- [D. Brundage et al. **arXiv** 2022](https://arxiv.org/abs/2203.13888) - [A. Marcolini et al. **SoftwareX** 2022](https://www.sciencedirect.com/science/article/pii/S2352711022001558) - [M. Rahman et al. **Bioengineering** 2022](https://www.mdpi.com/2306-5354/9/8/335) - [C. Lama et al. **bioRxiv** 2022](https://www.biorxiv.org/content/10.1101/2022.09.28.509751v1.full) -- [D. Brundage et al. **arXiv** 2022](https://arxiv.org/abs/2203.13888) -- [S. Orsulic et al. **Frontiers in Oncology** 2022](https://www.frontiersin.org/articles/10.3389/fonc.2022.924945/full) -- [J. Linares et al. **Molecular Cell** 2021](https://www.cell.com/molecular-cell/fulltext/S1097-2765(21)00729-2) +- the list continues [**here 🔗 for 2023 and onwards**](https://scholar.google.com/scholar?oi=bibs&hl=en&cites=1157052756975292108) # Users From 0031f6e3a84eadd9c963f0e69b6ac2a64decc732 Mon Sep 17 00:00:00 2001 From: Dana-Farber Date: Wed, 8 Feb 2023 11:09:05 -0500 Subject: [PATCH 05/39] Update README.md --- README.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 4bde3eb8..189ad8c6 100644 --- a/README.md +++ b/README.md @@ -1,27 +1,27 @@ -🤖đŸ”Ŧ **PathML: Tools for computational pathology.** +🤖đŸ”Ŧ **PathML: Tools for computational pathology** -⭐ **PathML objective is to lower the barrier to entry to digital pathology.** +[![Downloads](https://pepy.tech/badge/pathml)](https://pepy.tech/project/pathml) +[![Documentation Status](https://readthedocs.org/projects/pathml/badge/?version=latest)](https://pathml.readthedocs.io/en/latest/?badge=latest) +[![codecov](https://codecov.io/gh/Dana-Farber-AIOS/pathml/branch/master/graph/badge.svg?token=UHSQPTM28Y)](https://codecov.io/gh/Dana-Farber-AIOS/pathml) +[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +[![PyPI version](https://img.shields.io/pypi/v/pathml)](https://pypi.org/project/pathml/) -ℹī¸ Imaging datasets in cancer research are growing exponentially in both quantity and information density. These massive datasets may enable derivation of insights for cancer research and clinical care, but only if researchers are equipped with the tools to leverage advanced computational analysis approaches such as machine learning and artificial intelligence. In this work, we highlight three themes to guide development of such computational tools: scalability, standardization, and ease of use. We then apply these principles to develop PathML, a general-purpose research toolkit for computational pathology. We describe the design of the PathML framework and demonstrate applications in diverse use cases. - -🚀 The fastest way to get started? `docker pull pathml/pathml && docker run -it -p 8888:8888 pathml/pathml` +⭐ **PathML objective is to lower the barrier to entry to digital pathology** - +Imaging datasets in cancer research are growing exponentially in both quantity and information density. These massive datasets may enable derivation of insights for cancer research and clinical care, but only if researchers are equipped with the tools to leverage advanced computational analysis approaches such as machine learning and artificial intelligence. In this work, we highlight three themes to guide development of such computational tools: scalability, standardization, and ease of use. We then apply these principles to develop PathML, a general-purpose research toolkit for computational pathology. We describe the design of the PathML framework and demonstrate applications in diverse use cases. - +🚀 **The fastest way to get started?** -[![Documentation Status](https://readthedocs.org/projects/pathml/badge/?version=latest)](https://pathml.readthedocs.io/en/latest/?badge=latest) -[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) -[![PyPI version](https://img.shields.io/pypi/v/pathml)](https://pypi.org/project/pathml/) -[![Downloads](https://pepy.tech/badge/pathml)](https://pepy.tech/project/pathml) -[![codecov](https://codecov.io/gh/Dana-Farber-AIOS/pathml/branch/master/graph/badge.svg?token=UHSQPTM28Y)](https://codecov.io/gh/Dana-Farber-AIOS/pathml) + docker pull pathml/pathml && docker run -it -p 8888:8888 pathml/pathml | Branch | Test status | | ------ | ------------- | | master | ![tests](https://github.com/Dana-Farber-AIOS/pathml/actions/workflows/tests-conda.yml/badge.svg?branch=master) | | dev | ![tests](https://github.com/Dana-Farber-AIOS/pathml/actions/workflows/tests-conda.yml/badge.svg?branch=dev) | -An open-source toolkit for computational pathology and machine learning. + + + **View [documentation](https://pathml.readthedocs.io/en/latest/)** From 57782ab8a9aa720137b531c56a65afcb47aa5f5f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 11 Feb 2023 00:30:52 +0000 Subject: [PATCH 06/39] Bump ipython from 7.31.1 to 8.10.0 in /docs Bumps [ipython](https://github.com/ipython/ipython) from 7.31.1 to 8.10.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](https://github.com/ipython/ipython/compare/7.31.1...8.10.0) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- docs/readthedocs-requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/readthedocs-requirements.txt b/docs/readthedocs-requirements.txt index 831e134d..e2c1583d 100644 --- a/docs/readthedocs-requirements.txt +++ b/docs/readthedocs-requirements.txt @@ -3,5 +3,5 @@ nbsphinx==0.8.8 nbsphinx-link==1.3.0 sphinx-rtd-theme==1.0.0 sphinx-autoapi==1.8.4 -ipython==7.31.1 +ipython==8.10.0 sphinx-copybutton==0.4.0 From e2c29b901e23296e243f48e09c1808932802923f Mon Sep 17 00:00:00 2001 From: jacob-rosenthal <53529525+jacob-rosenthal@users.noreply.github.com> Date: Wed, 19 Apr 2023 13:47:14 -0400 Subject: [PATCH 07/39] bump isort version for python 3.7 compatibility --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7320bf2f..e096e8b3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -16,7 +16,7 @@ repos: - id: black - repo: https://github.com/timothycrosley/isort - rev: 5.10.1 + rev: 5.11.5 hooks: - id: isort From 8553ee5791ba2afbbf97139e732ca2cc0ec4f395 Mon Sep 17 00:00:00 2001 From: Jacob Rosenthal <53529525+jacob-rosenthal@users.noreply.github.com> Date: Fri, 5 May 2023 14:26:36 -0400 Subject: [PATCH 08/39] Update README.md Add instructions for Google colab --- README.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/README.md b/README.md index 189ad8c6..9b176bc4 100644 --- a/README.md +++ b/README.md @@ -133,6 +133,23 @@ Note that these instructions assume that there are no other processes using port Please refer to the `Docker run` [documentation](https://docs.docker.com/engine/reference/run/) for further instructions on accessing the container, e.g. for mounting volumes to access files on a local machine from within the container. +## Option 4: Google Colab + +To get PathML running in a Colab environment: + +```` +!pip install openslide-python +!apt-get install openslide-tools +!apt-get install openjdk-8-jdk-headless -qq > /dev/null +os.environ["JAVA_HOME"] = "/usr/lib/jvm/java-8-openjdk-amd64" +!update-alternatives --set java /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java +!java -version +!pip install pathml +```` + +*Thanks to all of our open-source collaborators for helping maintain these installation instructions!* +*Please open an issue for any bugs or other problems during installation process.* + ## CUDA To use GPU acceleration for model training or other tasks, you must install CUDA. From 9631286979739ddbc6f08ffff00f03c5685bde56 Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Tue, 9 May 2023 15:34:17 -0400 Subject: [PATCH 09/39] Update readthedocs-requirements.txt Added urllib3 --- docs/readthedocs-requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/readthedocs-requirements.txt b/docs/readthedocs-requirements.txt index e2c1583d..443d89e2 100644 --- a/docs/readthedocs-requirements.txt +++ b/docs/readthedocs-requirements.txt @@ -5,3 +5,4 @@ sphinx-rtd-theme==1.0.0 sphinx-autoapi==1.8.4 ipython==8.10.0 sphinx-copybutton==0.4.0 +urllib3==1.26.15 From 42c4cc8b20343cbc55fafc9e366aab75c05add87 Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Tue, 9 May 2023 15:56:29 -0400 Subject: [PATCH 10/39] Update .readthedocs.yaml Added new build, due to conflicts with urllib3 recent updates. --- .readthedocs.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 86d61526..d747bd11 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -5,6 +5,12 @@ # Required version: 2 + +build: + os: ubuntu-22.04 + tools: + python: "3.11" + # Build documentation with Sphinx sphinx: configuration: docs/source/conf.py From 912834f8116e594e384b4faea77cc25b3d756450 Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Tue, 9 May 2023 15:59:48 -0400 Subject: [PATCH 11/39] Update .readthedocs.yaml Modified file --- .readthedocs.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index d747bd11..ec0cbe3d 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,8 +8,6 @@ version: 2 build: os: ubuntu-22.04 - tools: - python: "3.11" # Build documentation with Sphinx sphinx: From 927c86e34ea2bf4c3af6247b0630654ca68f916e Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Tue, 9 May 2023 16:10:09 -0400 Subject: [PATCH 12/39] Update .readthedocs.yaml added build --- .readthedocs.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index ec0cbe3d..02377793 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -5,9 +5,10 @@ # Required version: 2 - build: os: ubuntu-22.04 + tools: + python: "3.8" # Build documentation with Sphinx sphinx: @@ -16,6 +17,5 @@ sphinx: fail_on_warning: false python: - version: "3.8" install: - requirements: docs/readthedocs-requirements.txt From eb62e298398cab9e28ed496bfc2391e613c9d0aa Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Tue, 9 May 2023 16:13:58 -0400 Subject: [PATCH 13/39] Update readthedocs-requirements.txt --- docs/readthedocs-requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/readthedocs-requirements.txt b/docs/readthedocs-requirements.txt index 443d89e2..b672810f 100644 --- a/docs/readthedocs-requirements.txt +++ b/docs/readthedocs-requirements.txt @@ -5,4 +5,4 @@ sphinx-rtd-theme==1.0.0 sphinx-autoapi==1.8.4 ipython==8.10.0 sphinx-copybutton==0.4.0 -urllib3==1.26.15 + From 837e8ec547a959bcce68f1f7abfdd948bb10e9d2 Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Wed, 17 May 2023 14:39:00 -0400 Subject: [PATCH 14/39] Update _version.py Update version --- pathml/_version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pathml/_version.py b/pathml/_version.py index b91684f4..2704c284 100644 --- a/pathml/_version.py +++ b/pathml/_version.py @@ -3,4 +3,4 @@ License: GNU GPL 2.0 """ -__version__ = "2.1.0" +__version__ = "2.1.1" From 8b8838042f1b284b1c04aacb7c52af458a386f62 Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Thu, 18 May 2023 15:59:55 -0400 Subject: [PATCH 15/39] Update publish-to-pypi.yml Updated Ubuntu OS --- .github/workflows/publish-to-pypi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index dd5dd367..fcd2bf9a 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -7,7 +7,7 @@ on: jobs: build-n-publish: name: Build and publish PathML distribution to PyPI and TestPyPI - runs-on: ubuntu-18.04 + runs-on: ubuntu-latest steps: - uses: actions/checkout@master - name: Set up Python 3.9 From 9c91bc5cd16c2f19bfb87e88adc9330045b2f49c Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Mon, 22 May 2023 12:54:46 -0400 Subject: [PATCH 16/39] Update publish-to-pypi.yml Changed ubuntu version to 22.04 --- .github/workflows/publish-to-pypi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index fcd2bf9a..7b0c1d4d 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -7,7 +7,7 @@ on: jobs: build-n-publish: name: Build and publish PathML distribution to PyPI and TestPyPI - runs-on: ubuntu-latest + runs-on: ubuntu-22.04 steps: - uses: actions/checkout@master - name: Set up Python 3.9 From 1ac207f434d5ab14b3ce13da54697a85cde053c9 Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Mon, 22 May 2023 13:15:46 -0400 Subject: [PATCH 17/39] Update publish-to-pypi.yml --- .github/workflows/publish-to-pypi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index 7b0c1d4d..9f29185f 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -7,7 +7,7 @@ on: jobs: build-n-publish: name: Build and publish PathML distribution to PyPI and TestPyPI - runs-on: ubuntu-22.04 + runs-on: ubuntu-20.04 steps: - uses: actions/checkout@master - name: Set up Python 3.9 From f289495a25a81625cbcda300a8e8a7d9ac98116f Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Mon, 22 May 2023 17:38:02 -0400 Subject: [PATCH 18/39] Update publish-to-pypi.yml --- .github/workflows/publish-to-pypi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index 9f29185f..dd5dd367 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -7,7 +7,7 @@ on: jobs: build-n-publish: name: Build and publish PathML distribution to PyPI and TestPyPI - runs-on: ubuntu-20.04 + runs-on: ubuntu-18.04 steps: - uses: actions/checkout@master - name: Set up Python 3.9 From 05aefd83be1250b5401ab540f2bb26bca9525bfb Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Mon, 22 May 2023 18:09:02 -0400 Subject: [PATCH 19/39] Update publish-to-pypi.yml Changed Ubuntu version --- .github/workflows/publish-to-pypi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index dd5dd367..fcd2bf9a 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -7,7 +7,7 @@ on: jobs: build-n-publish: name: Build and publish PathML distribution to PyPI and TestPyPI - runs-on: ubuntu-18.04 + runs-on: ubuntu-latest steps: - uses: actions/checkout@master - name: Set up Python 3.9 From 030618dfe8ba7c7c9a832ce91d60903734fe851d Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Mon, 22 May 2023 18:17:56 -0400 Subject: [PATCH 20/39] Update tests-conda.yml Update GitHub Actions workflow to use mamba for dependency management --- .github/workflows/tests-conda.yml | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/.github/workflows/tests-conda.yml b/.github/workflows/tests-conda.yml index 05401f41..e35ae2a8 100644 --- a/.github/workflows/tests-conda.yml +++ b/.github/workflows/tests-conda.yml @@ -24,33 +24,32 @@ jobs: uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} - # Test matrix by printing the current Python version - name: Display Python version run: python -c "import sys; print(sys.version)" - name: Install dependencies shell: bash -l {0} run: | sudo apt-get update - # install openslide sudo apt-get install openslide-tools - # install pandoc for making documentation sudo apt-get install pandoc - name: Setup Miniconda - # You may pin to the exact commit or the version. - # uses: conda-incubator/setup-miniconda@f4c00b0ec69bdc87b1ab4972613558dd9f4f36f3 - uses: conda-incubator/setup-miniconda@v2.0.0 + uses: conda-incubator/setup-miniconda@v2 with: - add_pip_as_python_dependency: false - environment-file: environment.yml + auto-activate-base: false activate-environment: pathml + environment-file: environment.yml + mamba-version: "*" python-version: ${{ matrix.python-version }} + - name: Install dependencies with mamba + run: | + mamba env update --file environment.yml --name pathml - name: Conda info shell: bash -l {0} run: | conda info conda list - - name: pip install pathml - shell: bash -l {0} + - name: Install PathML + shell: bash -l {0} run: pip install -e . - name: disk usage shell: bash -l {0} From 0f539687a0de6294660ad8ce313149ff40d43ed4 Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Mon, 22 May 2023 18:42:21 -0400 Subject: [PATCH 21/39] Update tests-conda.yml --- .github/workflows/tests-conda.yml | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests-conda.yml b/.github/workflows/tests-conda.yml index e35ae2a8..0d2de86c 100644 --- a/.github/workflows/tests-conda.yml +++ b/.github/workflows/tests-conda.yml @@ -17,6 +17,7 @@ jobs: max-parallel: 5 matrix: python-version: [3.8, 3.9] + timeout-minutes: 60 # add a timeout steps: - uses: actions/checkout@v2 @@ -40,9 +41,17 @@ jobs: environment-file: environment.yml mamba-version: "*" python-version: ${{ matrix.python-version }} - - name: Install dependencies with mamba + - name: Debugging run: | - mamba env update --file environment.yml --name pathml + echo "Printing the environment.yml file..." + cat environment.yml + echo "Checking the status of mamba..." + mamba --version + echo "Checking the available disk space..." + df -h + - name: Install dependencies with mamba + shell: bash -l {0} + run: mamba env update --file environment.yml --name pathml - name: Conda info shell: bash -l {0} run: | From c95fd1d1a50bcd8ba97975df84ef357097886931 Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Mon, 22 May 2023 19:26:38 -0400 Subject: [PATCH 22/39] Update tests-conda.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Excluding python=3.9 to resolve the following issue is github action runs: Could not solve for environment specs The following packages are incompatible ├─ python 3.8 is requested and can be installed; └─ python 3.9** is uninstallable because it conflicts with any installable versions previously reported. --- .github/workflows/tests-conda.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests-conda.yml b/.github/workflows/tests-conda.yml index 0d2de86c..619c3f9a 100644 --- a/.github/workflows/tests-conda.yml +++ b/.github/workflows/tests-conda.yml @@ -16,7 +16,7 @@ jobs: strategy: max-parallel: 5 matrix: - python-version: [3.8, 3.9] + python-version: [3.8] timeout-minutes: 60 # add a timeout steps: From 47e0ae03982f2126c0036f653c3b6f2f2e817484 Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Mon, 22 May 2023 19:49:30 -0400 Subject: [PATCH 23/39] Update tests-conda.yml Added python 3.9 to test the environment --- .github/workflows/tests-conda.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/tests-conda.yml b/.github/workflows/tests-conda.yml index 619c3f9a..0d2de86c 100644 --- a/.github/workflows/tests-conda.yml +++ b/.github/workflows/tests-conda.yml @@ -16,7 +16,7 @@ jobs: strategy: max-parallel: 5 matrix: - python-version: [3.8] + python-version: [3.8, 3.9] timeout-minutes: 60 # add a timeout steps: From 735611fcc71e2b67272c3b9294c7d418f5fb6752 Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Mon, 22 May 2023 19:51:35 -0400 Subject: [PATCH 24/39] Update environment.yml Excluding python 3.8 as requirement --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 22754c02..9c82aa8c 100644 --- a/environment.yml +++ b/environment.yml @@ -6,7 +6,7 @@ channels: dependencies: - pip==21.3.1 - - python==3.8 +# - python==3.8 - numpy==1.19.5 - scipy==1.7.3 - scikit-image==0.18.3 From b3a05355f4d17e809492da24dc0435a2b2dfaea1 Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Fri, 26 May 2023 12:10:53 -0400 Subject: [PATCH 25/39] Update environment.yml Excluded python version as dependency --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 22754c02..9c82aa8c 100644 --- a/environment.yml +++ b/environment.yml @@ -6,7 +6,7 @@ channels: dependencies: - pip==21.3.1 - - python==3.8 +# - python==3.8 - numpy==1.19.5 - scipy==1.7.3 - scikit-image==0.18.3 From 312c1fc0078c5eae3b4e0098dfaaa372c682754a Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Fri, 26 May 2023 12:30:46 -0400 Subject: [PATCH 26/39] Update environment.yml Exclude python-spams dependency --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 9c82aa8c..757d42a4 100644 --- a/environment.yml +++ b/environment.yml @@ -11,7 +11,7 @@ dependencies: - scipy==1.7.3 - scikit-image==0.18.3 - matplotlib==3.5.1 - - python-spams==2.6.1 +# - python-spams==2.6.1 - openjdk==8.0.152 - pytorch==1.10.1 - h5py==3.1.0 From 3b82262e36c7a6777b01201bd7c9995e7660823d Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Fri, 26 May 2023 12:47:32 -0400 Subject: [PATCH 27/39] Update tests-conda.yml Replaced conda with mamba --- .github/workflows/tests-conda.yml | 28 ++++++++++++++++++---------- 1 file changed, 18 insertions(+), 10 deletions(-) diff --git a/.github/workflows/tests-conda.yml b/.github/workflows/tests-conda.yml index 05401f41..0d2de86c 100644 --- a/.github/workflows/tests-conda.yml +++ b/.github/workflows/tests-conda.yml @@ -17,6 +17,7 @@ jobs: max-parallel: 5 matrix: python-version: [3.8, 3.9] + timeout-minutes: 60 # add a timeout steps: - uses: actions/checkout@v2 @@ -24,33 +25,40 @@ jobs: uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} - # Test matrix by printing the current Python version - name: Display Python version run: python -c "import sys; print(sys.version)" - name: Install dependencies shell: bash -l {0} run: | sudo apt-get update - # install openslide sudo apt-get install openslide-tools - # install pandoc for making documentation sudo apt-get install pandoc - name: Setup Miniconda - # You may pin to the exact commit or the version. - # uses: conda-incubator/setup-miniconda@f4c00b0ec69bdc87b1ab4972613558dd9f4f36f3 - uses: conda-incubator/setup-miniconda@v2.0.0 + uses: conda-incubator/setup-miniconda@v2 with: - add_pip_as_python_dependency: false - environment-file: environment.yml + auto-activate-base: false activate-environment: pathml + environment-file: environment.yml + mamba-version: "*" python-version: ${{ matrix.python-version }} + - name: Debugging + run: | + echo "Printing the environment.yml file..." + cat environment.yml + echo "Checking the status of mamba..." + mamba --version + echo "Checking the available disk space..." + df -h + - name: Install dependencies with mamba + shell: bash -l {0} + run: mamba env update --file environment.yml --name pathml - name: Conda info shell: bash -l {0} run: | conda info conda list - - name: pip install pathml - shell: bash -l {0} + - name: Install PathML + shell: bash -l {0} run: pip install -e . - name: disk usage shell: bash -l {0} From 25dac4a040f8e17471f8471e383e9407ee41c1a7 Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Fri, 26 May 2023 13:26:07 -0400 Subject: [PATCH 28/39] Update tests-conda.yml Using setup-micromamba to setup environment, installing python-spams. --- .github/workflows/tests-conda.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/tests-conda.yml b/.github/workflows/tests-conda.yml index 0d2de86c..8b914442 100644 --- a/.github/workflows/tests-conda.yml +++ b/.github/workflows/tests-conda.yml @@ -34,7 +34,7 @@ jobs: sudo apt-get install openslide-tools sudo apt-get install pandoc - name: Setup Miniconda - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v1 with: auto-activate-base: false activate-environment: pathml @@ -60,6 +60,9 @@ jobs: - name: Install PathML shell: bash -l {0} run: pip install -e . + - name: Install python-spams + shell: bash -l {0} + run: pip install python-spams - name: disk usage shell: bash -l {0} run: | From 7670a1250f3af3f13a275f29d3df55e8be1d9a6e Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Fri, 26 May 2023 13:59:06 -0400 Subject: [PATCH 29/39] Update tests-conda.yml Added micromamba to setup environment --- .github/workflows/tests-conda.yml | 50 ++++++++++++++++++------------- 1 file changed, 30 insertions(+), 20 deletions(-) diff --git a/.github/workflows/tests-conda.yml b/.github/workflows/tests-conda.yml index 8b914442..6227cced 100644 --- a/.github/workflows/tests-conda.yml +++ b/.github/workflows/tests-conda.yml @@ -17,31 +17,34 @@ jobs: max-parallel: 5 matrix: python-version: [3.8, 3.9] - timeout-minutes: 60 # add a timeout + timeout-minutes: 60 steps: - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} + - name: Display Python version run: python -c "import sys; print(sys.version)" - - name: Install dependencies + + - name: Install system dependencies shell: bash -l {0} run: | sudo apt-get update - sudo apt-get install openslide-tools - sudo apt-get install pandoc - - name: Setup Miniconda - uses: conda-incubator/setup-miniconda@v1 + sudo apt-get install -y openslide-tools pandoc + + - name: Setup Micromamba + uses: mamba-org/setup-micromamba@v1 with: - auto-activate-base: false - activate-environment: pathml environment-file: environment.yml - mamba-version: "*" - python-version: ${{ matrix.python-version }} + micromamba-version: latest + activate-environment: pathml + - name: Debugging + shell: bash -l {0} run: | echo "Printing the environment.yml file..." cat environment.yml @@ -49,30 +52,36 @@ jobs: mamba --version echo "Checking the available disk space..." df -h - - name: Install dependencies with mamba - shell: bash -l {0} - run: mamba env update --file environment.yml --name pathml + - name: Conda info shell: bash -l {0} run: | conda info conda list + + - name: Install dependencies with mamba + run: mamba env update --file environment.yml --name pathml + + - name: Install python-spams + run: micromamba install -y -n base -c conda-forge python-spams + + - name: Install PathML - shell: bash -l {0} + shell: bash -l {0} run: pip install -e . - - name: Install python-spams - shell: bash -l {0} - run: pip install python-spams - - name: disk usage + + - name: Disk usage shell: bash -l {0} run: | - sudo df -h - sudo du -h + df -h + du -sh + - name: Test with pytest and generate coverage report shell: bash -l {0} run: | coverage run -m pytest -m "not slow" coverage xml + - name: Upload coverage to Codecov uses: codecov/codecov-action@v2 with: @@ -82,6 +91,7 @@ jobs: files: ./coverage.xml name: codecov-umbrella verbose: true + - name: Compile docs shell: bash -l {0} run: | From dfc21d5995dffe2e2944ac02b27b4c588742717d Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Fri, 26 May 2023 14:13:48 -0400 Subject: [PATCH 30/39] Update tests-conda.yml rollback to mamba, couldn't resolve openjdk 8 when using micromamba --- .github/workflows/tests-conda.yml | 52 +++++++++++++------------------ 1 file changed, 22 insertions(+), 30 deletions(-) diff --git a/.github/workflows/tests-conda.yml b/.github/workflows/tests-conda.yml index 6227cced..1b193022 100644 --- a/.github/workflows/tests-conda.yml +++ b/.github/workflows/tests-conda.yml @@ -17,34 +17,31 @@ jobs: max-parallel: 5 matrix: python-version: [3.8, 3.9] - timeout-minutes: 60 + timeout-minutes: 60 # add a timeout steps: - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} - - name: Display Python version run: python -c "import sys; print(sys.version)" - - - name: Install system dependencies + - name: Install dependencies shell: bash -l {0} run: | sudo apt-get update - sudo apt-get install -y openslide-tools pandoc - - - name: Setup Micromamba - uses: mamba-org/setup-micromamba@v1 + sudo apt-get install openslide-tools + sudo apt-get install pandoc + - name: Setup Miniconda + uses: conda-incubator/setup-miniconda@v2 with: - environment-file: environment.yml - micromamba-version: latest + auto-activate-base: false activate-environment: pathml - + environment-file: environment.yml + mamba-version: "*" + python-version: ${{ matrix.python-version }} - name: Debugging - shell: bash -l {0} run: | echo "Printing the environment.yml file..." cat environment.yml @@ -52,36 +49,32 @@ jobs: mamba --version echo "Checking the available disk space..." df -h - + - name: Install dependencies with mamba + shell: bash -l {0} + run: mamba env update --file environment.yml --name pathml - name: Conda info shell: bash -l {0} run: | conda info conda list - - - name: Install dependencies with mamba - run: mamba env update --file environment.yml --name pathml - - - name: Install python-spams - run: micromamba install -y -n base -c conda-forge python-spams - - - name: Install PathML - shell: bash -l {0} + shell: bash -l {0} run: pip install -e . - - - name: Disk usage + + - name: Install python-spams + shell: bash -l {0} + run: pip install python-spams + + - name: disk usage shell: bash -l {0} run: | - df -h - du -sh - + sudo df -h + sudo du -h - name: Test with pytest and generate coverage report shell: bash -l {0} run: | coverage run -m pytest -m "not slow" coverage xml - - name: Upload coverage to Codecov uses: codecov/codecov-action@v2 with: @@ -91,7 +84,6 @@ jobs: files: ./coverage.xml name: codecov-umbrella verbose: true - - name: Compile docs shell: bash -l {0} run: | From b630aec07956a488717039bfb8e811f4cc24abc1 Mon Sep 17 00:00:00 2001 From: Jacob Rosenthal <53529525+jacob-rosenthal@users.noreply.github.com> Date: Mon, 29 May 2023 21:15:20 -0400 Subject: [PATCH 31/39] Remove commented out lines --- environment.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/environment.yml b/environment.yml index 757d42a4..3910502f 100644 --- a/environment.yml +++ b/environment.yml @@ -6,12 +6,10 @@ channels: dependencies: - pip==21.3.1 -# - python==3.8 - numpy==1.19.5 - scipy==1.7.3 - scikit-image==0.18.3 - matplotlib==3.5.1 -# - python-spams==2.6.1 - openjdk==8.0.152 - pytorch==1.10.1 - h5py==3.1.0 From 935a63097b4e345507c3a63d3a55b82eb93286c7 Mon Sep 17 00:00:00 2001 From: jacob-rosenthal <53529525+jacob-rosenthal@users.noreply.github.com> Date: Mon, 29 May 2023 22:41:07 -0400 Subject: [PATCH 32/39] allow manual workflow triggering --- .github/workflows/publish-to-pypi.yml | 1 + .github/workflows/tests-conda.yml | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index fcd2bf9a..ad759638 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -1,6 +1,7 @@ name: Publish PathML distribution to PyPI and TestPyPI on: + workflow_dispatch: release: types: [published] diff --git a/.github/workflows/tests-conda.yml b/.github/workflows/tests-conda.yml index 1b193022..53a8d93a 100644 --- a/.github/workflows/tests-conda.yml +++ b/.github/workflows/tests-conda.yml @@ -1,6 +1,7 @@ name: Tests -on: +on: + workflow_dispatch: pull_request: branches: - dev From 1e32970037772f176c90bf534d2b49cc57c35e2e Mon Sep 17 00:00:00 2001 From: sreekarreddydfci <91486875+sreekarreddydfci@users.noreply.github.com> Date: Wed, 26 Jul 2023 15:01:09 -0500 Subject: [PATCH 33/39] Update environment.yml (#361) Update openslide-python to v1.2.0 to resolve 'ANTIALIAS' AttributeError This commit upgrades openslide-python to version 1.2.0 to address an AttributeError related to the 'ANTIALIAS' attribute in the PIL.Image module. The issue was triggered due to the deprecation of 'ANTIALIAS' in Pillow v10.0.0. --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 3910502f..457f49b2 100644 --- a/environment.yml +++ b/environment.yml @@ -24,7 +24,7 @@ dependencies: - protobuf==3.20.1 - deepcell==0.11.0 - opencv-contrib-python==4.5.3.56 - - openslide-python==1.1.2 + - openslide-python==1.2.0 - scanpy==1.8.2 - anndata==0.7.8 - tqdm==4.62.3 From 68a722441d883daf349aa6333eec9148c553e089 Mon Sep 17 00:00:00 2001 From: Dana-Farber Date: Wed, 23 Aug 2023 10:09:34 -0400 Subject: [PATCH 34/39] Update README.md updated the Download counter button --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9b176bc4..ade81e2d 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ 🤖đŸ”Ŧ **PathML: Tools for computational pathology** -[![Downloads](https://pepy.tech/badge/pathml)](https://pepy.tech/project/pathml) +[![Downloads](https://static.pepy.tech/badge/pathml)](https://pepy.tech/project/pathml) [![Documentation Status](https://readthedocs.org/projects/pathml/badge/?version=latest)](https://pathml.readthedocs.io/en/latest/?badge=latest) [![codecov](https://codecov.io/gh/Dana-Farber-AIOS/pathml/branch/master/graph/badge.svg?token=UHSQPTM28Y)](https://codecov.io/gh/Dana-Farber-AIOS/pathml) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) From cda8fa7d50f4581db7dfdf3327d19dc3c1469665 Mon Sep 17 00:00:00 2001 From: jamesgwen Date: Tue, 17 Oct 2023 07:26:58 -0700 Subject: [PATCH 35/39] changing opencv req to 1.3.1 --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 457f49b2..c776c7af 100644 --- a/environment.yml +++ b/environment.yml @@ -24,7 +24,7 @@ dependencies: - protobuf==3.20.1 - deepcell==0.11.0 - opencv-contrib-python==4.5.3.56 - - openslide-python==1.2.0 + - openslide-python==1.3.1 - scanpy==1.8.2 - anndata==0.7.8 - tqdm==4.62.3 From a998708cfdf4ae26f81f8085e5a317603f5b504b Mon Sep 17 00:00:00 2001 From: jamesgwen Date: Tue, 17 Oct 2023 07:34:17 -0700 Subject: [PATCH 36/39] fixing comment from last commit: updating openslide to 1.3.1 --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index c776c7af..26300cb6 100644 --- a/environment.yml +++ b/environment.yml @@ -24,7 +24,7 @@ dependencies: - protobuf==3.20.1 - deepcell==0.11.0 - opencv-contrib-python==4.5.3.56 - - openslide-python==1.3.1 + - openslide-python==1.3.1 #former 1.2.0 - scanpy==1.8.2 - anndata==0.7.8 - tqdm==4.62.3 From f65c72e1ff4ee92573a499028eb2821ed4fe62bb Mon Sep 17 00:00:00 2001 From: jamesgwen Date: Tue, 17 Oct 2023 09:13:07 -0700 Subject: [PATCH 37/39] adjusting comments --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 26300cb6..0c64028f 100644 --- a/environment.yml +++ b/environment.yml @@ -24,7 +24,7 @@ dependencies: - protobuf==3.20.1 - deepcell==0.11.0 - opencv-contrib-python==4.5.3.56 - - openslide-python==1.3.1 #former 1.2.0 + - openslide-python==1.3.1 # upate to openslide 4.0.0 - scanpy==1.8.2 - anndata==0.7.8 - tqdm==4.62.3 From b929b6711f60f7a58c521760c4fdb075f2a18669 Mon Sep 17 00:00:00 2001 From: jamesgwen Date: Wed, 18 Oct 2023 09:41:42 -0700 Subject: [PATCH 38/39] adjusting read the docs requirements --- docs/readthedocs-requirements.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/readthedocs-requirements.txt b/docs/readthedocs-requirements.txt index b672810f..b83c548d 100644 --- a/docs/readthedocs-requirements.txt +++ b/docs/readthedocs-requirements.txt @@ -1,8 +1,8 @@ -sphinx==4.3.2 +sphinx==6.2.1 nbsphinx==0.8.8 nbsphinx-link==1.3.0 sphinx-rtd-theme==1.0.0 -sphinx-autoapi==1.8.4 +sphinx-autoapi==3.0.0 ipython==8.10.0 sphinx-copybutton==0.4.0 From c058c1db9e6e1eda3b11d6fe78d3b501524e555b Mon Sep 17 00:00:00 2001 From: jamesgwen Date: Wed, 18 Oct 2023 13:31:52 -0700 Subject: [PATCH 39/39] adjusting doc ddepen and miniconda version --- .github/workflows/tests-conda.yml | 5 ++++- docs/readthedocs-requirements.txt | 4 ++-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/tests-conda.yml b/.github/workflows/tests-conda.yml index 53a8d93a..c93c4213 100644 --- a/.github/workflows/tests-conda.yml +++ b/.github/workflows/tests-conda.yml @@ -40,7 +40,10 @@ jobs: auto-activate-base: false activate-environment: pathml environment-file: environment.yml - mamba-version: "*" + # mamba-version: "*" + miniforge-version: latest + use-mamba: true + channels: conda-forge python-version: ${{ matrix.python-version }} - name: Debugging run: | diff --git a/docs/readthedocs-requirements.txt b/docs/readthedocs-requirements.txt index b83c548d..95b9a3cc 100644 --- a/docs/readthedocs-requirements.txt +++ b/docs/readthedocs-requirements.txt @@ -1,7 +1,7 @@ -sphinx==6.2.1 +sphinx==7.1.2 nbsphinx==0.8.8 nbsphinx-link==1.3.0 -sphinx-rtd-theme==1.0.0 +sphinx-rtd-theme==1.3.0 sphinx-autoapi==3.0.0 ipython==8.10.0 sphinx-copybutton==0.4.0