From ea4d3b3a3dfe343397d7cb0d08ec6aeb2bdf38c9 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 22 Aug 2022 07:40:27 +0200 Subject: [PATCH 1/8] solve issue #409 of install --- README.md | 4 ++-- azure-pipelines.yml | 4 ++-- docs/content/installation.rst | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index eb0443ab..38cccdd9 100644 --- a/README.md +++ b/README.md @@ -70,7 +70,7 @@ Then activate the environment and install pygenometracks with mamba: ```bash conda activate pygenometracks -mamba install -c defaults -c bioconda -c conda-forge pygenometracks +mamba install -c bioconda -c conda-forge pygenometracks ``` or if you want a specific version: @@ -78,7 +78,7 @@ or if you want a specific version: ```bash conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.7 conda activate pygenometracks -mamba install -c defaults -c bioconda -c conda-forge pygenometracks=3.5 +mamba install -c bioconda -c conda-forge pygenometracks=3.5 ``` Also, pyGenomeTracks can be installed using pip diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 09e4e376..f93e6601 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -37,7 +37,7 @@ stages: cat requirements_CI.txt | awk -v v=$(matplotlib.version) '{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt conda create -n pygenometracks --yes -c conda-forge -c bioconda python=$(python.version) mamba source activate pygenometracks - mamba install --yes -c defaults -c conda-forge -c bioconda --file requirements_CI_updated.txt + mamba install --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt python setup.py install displayName: installing dependencies - script: | @@ -86,7 +86,7 @@ stages: cat requirements_CI.txt | awk -v v=$(matplotlib.version) '{if($0~/matplotlib/){$0="matplotlib =="v}; print}' > requirements_CI_updated.txt conda create -n pygenometracks --yes -c conda-forge -c bioconda python=$(python.version) mamba source activate pygenometracks - mamba install --yes -c defaults -c conda-forge -c bioconda --file requirements_CI_updated.txt + mamba install --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt python setup.py install displayName: installing dependencies - script: | diff --git a/docs/content/installation.rst b/docs/content/installation.rst index 0abff0ff..c1656594 100644 --- a/docs/content/installation.rst +++ b/docs/content/installation.rst @@ -60,7 +60,7 @@ Then activate the environment and install pygenometracks with mamba: .. code:: bash $ conda activate pygenometracks - $ mamba install -c defaults -c bioconda -c conda-forge pygenometracks + $ mamba install -c bioconda -c conda-forge pygenometracks or if you want a specific version: @@ -69,8 +69,8 @@ or if you want a specific version: .. code:: bash $ conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.7 - $ conda activate pygenometracks - $ mamba install -c defaults -c bioconda -c conda-forge pygenometracks=3.5 + $ conda activate pygenometracks + $ mamba install -c bioconda -c conda-forge pygenometracks=3.5 Command line installation using ``pip`` ----------------------------------------- From f0e1bfaa69f6d4e9476bc2b7f85f7f87845ed893 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 22 Aug 2022 09:02:39 +0200 Subject: [PATCH 2/8] temporarily exclude E275 --- azure-pipelines.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index f93e6601..b7eb1bde 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -91,7 +91,7 @@ stages: displayName: installing dependencies - script: | source activate pygenometracks - flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E712,W503 + flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E712,W503,E275 displayName: linting - script: | source activate pygenometracks From 62f8674ab5c1ef68c979fd6ac0731f5fda85590d Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 22 Aug 2022 09:12:03 +0200 Subject: [PATCH 3/8] only lint once at first --- azure-pipelines.yml | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index b7eb1bde..8f737532 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -2,7 +2,21 @@ pr: autoCancel: true stages: +- stage: lint + jobs: + - job: Linux + timeoutInMinutes: 0 + pool: + vmImage: 'Ubuntu-latest' + container: python:3.8 + steps: + - script: | + python -m pip install --user --upgrade flake8 + flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E712,W503,E275 + displayName: linting - stage: test + dependsOn: [lint] + condition: succeeded() jobs: - job: Linux timeoutInMinutes: 0 @@ -40,10 +54,6 @@ stages: mamba install --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt python setup.py install displayName: installing dependencies - - script: | - source activate pygenometracks - flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E712,W503 - displayName: linting - script: | source activate pygenometracks py.test pygenometracks --doctest-modules -n 4 @@ -89,10 +99,6 @@ stages: mamba install --yes -c conda-forge -c bioconda --file requirements_CI_updated.txt python setup.py install displayName: installing dependencies - - script: | - source activate pygenometracks - flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E712,W503,E275 - displayName: linting - script: | source activate pygenometracks py.test pygenometracks --doctest-modules -n 4 From f8de69f4946076f0e0f9abd8ad89f93d5c754376 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 22 Aug 2022 09:25:31 +0200 Subject: [PATCH 4/8] add .localbin --- azure-pipelines.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 8f737532..376d4726 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -10,8 +10,14 @@ stages: vmImage: 'Ubuntu-latest' container: python:3.8 steps: - - script: | + - bash: python -m pip install --user --upgrade flake8 + displayName: install flake8 + - bash: | + echo "##vso[task.prependpath].local/bin" + hash -r + displayName: Add .local/bin to PATH + - script: flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E712,W503,E275 displayName: linting - stage: test From 64baeb6d435430f5b72a30ba3dc4977b128724b3 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 22 Aug 2022 09:32:12 +0200 Subject: [PATCH 5/8] add home --- azure-pipelines.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 376d4726..6695ad06 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -10,13 +10,13 @@ stages: vmImage: 'Ubuntu-latest' container: python:3.8 steps: - - bash: - python -m pip install --user --upgrade flake8 - displayName: install flake8 - bash: | - echo "##vso[task.prependpath].local/bin" + echo "##vso[task.prependpath]$HOME/.local/bin" hash -r displayName: Add .local/bin to PATH + - bash: + python -m pip install --user --upgrade flake8 + displayName: install flake8 - script: flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E712,W503,E275 displayName: linting From fb018c603806e1f2c7d0a887fd187c4fe98ccc1b Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 22 Aug 2022 09:38:36 +0200 Subject: [PATCH 6/8] decrease version of gffutils temporarily --- requirements_CI.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_CI.txt b/requirements_CI.txt index fbc2a1ce..3b54df35 100644 --- a/requirements_CI.txt +++ b/requirements_CI.txt @@ -5,7 +5,7 @@ pybigwig >=0.3.16 future >=0.17.0 hicmatrix >=15 pysam >=0.14 -gffutils >=0.9 +gffutils >=0.9 <0.11 # This is waiting for release pybedtools >=0.8.1 tqdm >=4.20 bx-python >=0.8.13 From a1f1f0b2da5c8bdafb45320ab83ff7911e48c5ed Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 22 Aug 2022 09:50:33 +0200 Subject: [PATCH 7/8] fix gffutils --- requirements_CI.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_CI.txt b/requirements_CI.txt index 3b54df35..171ea891 100644 --- a/requirements_CI.txt +++ b/requirements_CI.txt @@ -5,7 +5,7 @@ pybigwig >=0.3.16 future >=0.17.0 hicmatrix >=15 pysam >=0.14 -gffutils >=0.9 <0.11 # This is waiting for release +gffutils ==0.10 # This is waiting for release pybedtools >=0.8.1 tqdm >=4.20 bx-python >=0.8.13 From 009d063c83b317c9f6af76c21f1ce54d84c23bd0 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 22 Aug 2022 10:01:43 +0200 Subject: [PATCH 8/8] fix gffutils to 0.9 --- requirements_CI.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_CI.txt b/requirements_CI.txt index 171ea891..1cc4e531 100644 --- a/requirements_CI.txt +++ b/requirements_CI.txt @@ -5,7 +5,7 @@ pybigwig >=0.3.16 future >=0.17.0 hicmatrix >=15 pysam >=0.14 -gffutils ==0.10 # This is waiting for release +gffutils ==0.9 # This is waiting for release pybedtools >=0.8.1 tqdm >=4.20 bx-python >=0.8.13