Merge pull request #410 from deeptools/fix_install_doc

solve issue #409 of install
deeptools · Sep 5, 2022 · 2085e04 · 2085e04
2 parents c42e74e + 009d063
commit 2085e04
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Showing 4 changed files with 28 additions and 16 deletions.
diff --git a/README.md b/README.md
@@ -70,15 +70,15 @@ 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:
 
 ```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
@@ -2,7 +2,27 @@ pr:
   autoCancel: true
 
 stages:
+- stage: lint
+  jobs:
+    - job: Linux
+      timeoutInMinutes: 0
+      pool:
+        vmImage: 'Ubuntu-latest'
+      container: python:3.8
+      steps:
+      - bash: |
+          echo "##vso[task.prependpath]$HOME/.local/bin"
+          hash -r
+        displayName: Add .local/bin to PATH
+      - bash:
+          python -m pip install --user --upgrade flake8
+        displayName: install flake8
+      - script:
+          flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E712,W503,E275
+        displayName: linting
 - stage: test
+  dependsOn: [lint]
+  condition: succeeded()
   jobs:
     - job: Linux
       timeoutInMinutes: 0
@@ -37,13 +57,9 @@ stages:
           cat requirements_CI.txt | awk -v v=$(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: |
-          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
@@ -86,13 +102,9 @@ 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: |
-          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

diff --git 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``
 -----------------------------------------

diff --git 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 # This is waiting for release
 pybedtools >=0.8.1
 tqdm >=4.20
 bx-python >=0.8.13