From dcc41e336d51859f1a2d37e910df3c4939c0b162 Mon Sep 17 00:00:00 2001 From: LouisFaure Date: Thu, 15 Feb 2024 21:35:07 +0100 Subject: [PATCH 1/3] Fixed adjustedText version to avoid error, changed tests to python 3.11 --- .github/workflows/load_test_upload.yml | 8 ++++---- README.md | 8 ++++---- docs/installation.rst | 4 ++-- docs/release_notes.rst | 8 ++++++-- requirements.txt | 2 +- 5 files changed, 17 insertions(+), 13 deletions(-) diff --git a/.github/workflows/load_test_upload.yml b/.github/workflows/load_test_upload.yml index edb0fd1..8cc7596 100644 --- a/.github/workflows/load_test_upload.yml +++ b/.github/workflows/load_test_upload.yml @@ -14,10 +14,10 @@ jobs: - uses: actions/checkout@v2 with: fetch-depth: 0 - - name: Set up Python 3.8 + - name: Set up Python 3.11 uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: 3.11 - name: Install package run: | pip install wheel @@ -35,10 +35,10 @@ jobs: - uses: actions/checkout@v2 with: fetch-depth: 0 - - name: Set up Python 3.8 + - name: Set up Python 3.11 uses: actions/setup-python@v2 with: - python-version: 3.8 + python-version: 3.11 - name: Install dependencies run: | sudo apt-get clean && sudo apt-get update diff --git a/README.md b/README.md index f813c16..193cca2 100644 --- a/README.md +++ b/README.md @@ -82,7 +82,7 @@ With all dependencies -`pp.find_overdispersed`, `tl.test_association`, `tl.fit`, `tl.test_fork`, `tl.activation`, `tl.test_association_covariate`, `tl.test_covariate`: Require R package mgcv interfaced via python package rpy2: - conda create -n scFates -c conda-forge -c r python=3.8 r-mgcv rpy2=3.4.2 -y + conda create -n scFates -c conda-forge -c r python=3.11 r-mgcv rpy2=3.4.2 -y conda activate scFates pip install scFates @@ -118,10 +118,10 @@ If you have a nvidia GPU, scFates can leverage CUDA computations for speedups fo `pp.filter_cells`, `pp.batch_correct`, `pp.diffusion`, `tl.tree`, `tl.cluster` -The latest version of rapids framework is required (at least 0.17) it is recommanded to create a new conda environment: +The latest version of rapids framework is required. Create the following conda environment: - conda create -n scFates-gpu -c rapidsai -c nvidia -c conda-forge -c defaults \ - cuml=21.12 cugraph=21.12 python=3.8 cudatoolkit=11.0 -y + conda create --solver=libmamba -n scFates-gpu -c rapidsai -c conda-forge -c nvidia \ + cuml=23.12 cugraph=23.12 python=3.10 cuda-version=11.2 conda activate scFates-gpu pip install git+https://github.com/j-bac/elpigraph-python.git pip install scFates diff --git a/docs/installation.rst b/docs/installation.rst index b7e0fe3..5d72df0 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -1,7 +1,7 @@ Installation ============ -scFates is continuously tested with python 3.7 and 3.8, it is recommended to use a Miniconda_ environment. +scFates is continuously tested with python 3.11, it is recommended to use a Miniconda_ environment. PyPI ---- @@ -20,7 +20,7 @@ With all dependencies - :func:`scFates.pp.find_overdispersed`, :func:`scFates.tl.test_association`, :func:`scFates.tl.fit`, :func:`scFates.tl.test_fork`, :func:`scFates.tl.activation`: Require R package mgcv interfaced via python package rpy2:: - conda create -n scFates -c conda-forge -c r python=3.8 r-mgcv rpy2 -y + conda create -n scFates -c conda-forge -c r python=3.11 r-mgcv rpy2 -y conda activate scFates pip install scFates diff --git a/docs/release_notes.rst b/docs/release_notes.rst index a485162..29ff671 100644 --- a/docs/release_notes.rst +++ b/docs/release_notes.rst @@ -4,11 +4,15 @@ Release Notes ============= -Version 1.0.6 :small:`August 26, 2566/2033` +Version 1.0.7 :small:`February 15, 2566/2024` +-------------------------------------------- +Fixed adjustedText version to avoid error, changed tests to python 3.11 + +Version 1.0.6 :small:`August 26, 2566/2023` ------------------------------------------- Fixed exception in :func:`scFates.tl.slide_cells` -Version 1.0.5 :small:`August 25, 2566/2033` +Version 1.0.5 :small:`August 25, 2566/2023` ------------------------------------------- Fix int and bool check when ordering segments in :func:`scFates.pl.trends`. diff --git a/requirements.txt b/requirements.txt index 8405e5c..07ed1ef 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ pandas<2.0 statsmodels>=0.11.1 matplotlib>=3.2.1 plotly>=4.8.1 -adjustText>=0.7.3 +adjustText==0.7.3 cycler>=0.10.0 python_igraph>=0.8.2 typing_extensions From a34977658a8e43b30ca9fdbd14318e224cb6e3e6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 11 Jan 2024 17:37:50 +0000 Subject: [PATCH 2/3] Bump jinja2 from 2.11.3 to 3.1.3 in /docs Bumps [jinja2](https://github.com/pallets/jinja) from 2.11.3 to 3.1.3. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/jinja/compare/2.11.3...3.1.3) --- updated-dependencies: - dependency-name: jinja2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index f46155f..636154b 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -9,7 +9,7 @@ matplotlib==3.3.1 sphinx==4.0.2 docutils readthedocs-sphinx-ext -Jinja2==2.11.3 +Jinja2==3.1.3 nbsphinx<0.8.7 ipython anndata From b1ad9c1476cbc22e4d434a84b9b2b304178863d1 Mon Sep 17 00:00:00 2001 From: LouisFaure Date: Thu, 15 Feb 2024 21:53:22 +0100 Subject: [PATCH 3/3] fix readthedocs build.os missing variable --- .readthedocs.yml | 6 +++++- docs/requirements.txt | 1 + 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index ecc079a..ca834bc 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -5,6 +5,11 @@ # Required version: 2 +build: + os: ubuntu-22.04 + tools: + python: "3.7" + # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py @@ -13,7 +18,6 @@ formats: - pdf python: - version: 3.7 install: - method: pip path: . diff --git a/docs/requirements.txt b/docs/requirements.txt index 636154b..4569632 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,3 +1,4 @@ +mock typing_extensions importlib_metadata sphinx_rtd_theme==0.5.2