Merge pull request #66 from antoniojbt/codex/fix-codecov-suggestions-regarding-pip-cache

Fix codefactor pip cache warnings

Author: antoniojbt

.github/workflows/tests.yml

@@ -20,9 +20,9 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install flake8 pytest
-          pip install -e .
+          pip install --no-cache-dir -r requirements.txt
+          pip install --no-cache-dir flake8 pytest
+          pip install --no-cache-dir -e .
       - name: Lint
         run: flake8 .
       - name: Test

requirements_pq_example.sh

@@ -38,7 +38,7 @@ conda install -y python=3.5
 # issues with cairo with python 3.7
 
 # Install project_quickstart and pq_example requirements:
-bash -c 'pip install project_quickstart ; \
+bash -c 'pip install --no-cache-dir project_quickstart ; \
          conda install -y r-docopt r-data.table r-ggplot2 r-stringr ; \
          conda install -y docopt pandas matplotlib scipy svgutils cairosvg ; \
          conda install -y r-svglite r-stargazer'

templates/examples/Dockerfile_pq_example_alpine

@@ -111,12 +111,12 @@ RUN conda update -y conda
 #    source deactivate'
 
 RUN conda install -y git ; \
-    pip install --upgrade pip cython numpy ; \
-    pip install pysam ; \
-    pip install pandas ; \
-    pip install ruffus ; \
+    pip install --no-cache-dir --upgrade pip cython numpy ; \
+    pip install --no-cache-dir pysam ; \
+    pip install --no-cache-dir pandas ; \
+    pip install --no-cache-dir ruffus ; \
     conda install sphinx ; \
-    pip install sphinxcontrib-bibtex ; \
+    pip install --no-cache-dir sphinxcontrib-bibtex ; \
     conda install -y -c r r=3.3 ; \
     conda install -y rpy2 ; \
     conda install -y readline ; \
@@ -127,15 +127,15 @@ RUN conda install -y git ; \
     conda install -y r-gdtools ; \
     R --vanilla -e 'source("https://bioconductor.org/biocLite.R") ; install.packages("svglite", repos = "http://cran.us.r-project.org") ; library("svglite")' ; \
     wget --no-check-certificate https://raw.githubusercontent.com/CGATOxford/cgat/master/requires.txt ; \
-    cat requires.txt | grep -v "#" | xargs -n 1 pip install ; \
+    cat requires.txt | grep -v "#" | xargs -n 1 pip install --no-cache-dir ; \
     conda install -y alignlib-lite ; \
     conda install -y bedtools ; \
     conda install -y pybedtools ; \
     conda install -y -c bioconda ucsc-wigtobigwig ; \
     conda install -y icu ; \
-    pip install git+git://github.com/AntonioJBT/CGATPipeline_core.git ; \
-    pip install git+git://github.com/AntonioJBT/project_quickstart.git ; \
-    pip install cgat 
+    pip install --no-cache-dir git+git://github.com/AntonioJBT/CGATPipeline_core.git ; \
+    pip install --no-cache-dir git+git://github.com/AntonioJBT/project_quickstart.git ; \
+    pip install --no-cache-dir cgat
 
 ############################
 # Default action to start in

templates/examples/Dockerfile_pq_example_ubuntu

@@ -90,12 +90,12 @@ RUN conda update -y conda
 
 # Install all packages needed:
 RUN conda install -y git ; \
-    pip install --upgrade pip cython numpy ; \
-    pip install pysam ; \
-    pip install pandas ; \
-    pip install ruffus ; \
+    pip install --no-cache-dir --upgrade pip cython numpy ; \
+    pip install --no-cache-dir pysam ; \
+    pip install --no-cache-dir pandas ; \
+    pip install --no-cache-dir ruffus ; \
     conda install -y sphinx ; \
-    pip install sphinxcontrib-bibtex ; \
+    pip install --no-cache-dir sphinxcontrib-bibtex ; \
     conda install -y -c r r=3.3 ; \
     conda install -y rpy2 ; \
     conda install -y readline ; \
@@ -106,16 +106,16 @@ RUN conda install -y git ; \
     conda install -y r-gdtools ; \
     R --vanilla -e 'source("https://bioconductor.org/biocLite.R") ; install.packages("svglite", repos = "http://cran.us.r-project.org") ; library("svglite")' ; \
     wget --no-check-certificate https://raw.githubusercontent.com/CGATOxford/cgat/master/requires.txt ; \
-    cat requires.txt | grep -v "#" | xargs -n 1 pip install ; \
+    cat requires.txt | grep -v "#" | xargs -n 1 pip install --no-cache-dir ; \
     conda install -y alignlib-lite ; \
     conda install -y bedtools ; \
     conda install -y pybedtools ; \
     conda install -y -c bioconda ucsc-wigtobigwig ; \
     conda install -y icu -c conda-forge
     conda install -y icu ; \
-    pip install sphinxcontrib-bibtex ; \
-    pip install git+git://github.com/AntonioJBT/CGATPipeline_core.git ; \
-    pip install git+git://github.com/AntonioJBT/project_quickstart.git 
+    pip install --no-cache-dir sphinxcontrib-bibtex ; \
+    pip install --no-cache-dir git+git://github.com/AntonioJBT/CGATPipeline_core.git ; \
+    pip install --no-cache-dir git+git://github.com/AntonioJBT/project_quickstart.git
 
 
 # This fails with continuumio/miniconda3 in this file and manually:

templates/project_template/.travis.yml

@@ -32,9 +32,9 @@ before_install:
 #  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew upgrade python; fi
 
 install:
-  - pip install -r requirements.txt # --use-mirrors errors in Py3.5
+  - pip install --no-cache-dir -r requirements.txt # --use-mirrors errors in Py3.5
   - python setup.py install
-  - pip install flake8
+  - pip install --no-cache-dir flake8
 #  - pip install coverage # coveralls.io continuously monitors test case coverage
 #  - pip install coveralls
 ################

templates/project_template/Dockerfile

@@ -81,9 +81,9 @@ RUN conda install python=3.6 \
     && conda install -y r
 
 # Install python packages:
-RUN pip install --upgrade pip numpy setuptools \
-    && pip install cython \
-    && pip install pandas \
+RUN pip install --no-cache-dir --upgrade pip numpy setuptools \
+    && pip install --no-cache-dir cython \
+    && pip install --no-cache-dir pandas \
     && pip list
 
 # Install project specific packages:
@@ -117,7 +117,7 @@ RUN conda install -y r-docopt=0.4.5 r-data.table=1.10.4 r-ggplot2=2.2.1 ; \
 # Install package of interest
 ##############################
 
-RUN pip install git+git://github.com/EpiCompBio/stats_utils.git
+RUN pip install --no-cache-dir git+git://github.com/EpiCompBio/stats_utils.git
 
 ############################
 # Default action to start in

templates/project_template/setup.py

@@ -11,7 +11,7 @@
 For Python 3.5
 Before packaging or installing run:
 
-    pip install -U pip twine check-manifest setuptools
+    pip install --no-cache-dir -U pip twine check-manifest setuptools
 
 TO DO: to add tests see https://python-packaging.readthedocs.io/en/latest/testing.html
 

tests/ref_files/pq_example/code/.travis.yml

@@ -32,9 +32,9 @@ before_install:
 #  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew upgrade python; fi
 
 install:
-  - pip install -r requirements.txt # --use-mirrors errors in Py3.5
+  - pip install --no-cache-dir -r requirements.txt # --use-mirrors errors in Py3.5
   - python setup.py install
-  - pip install flake8
+  - pip install --no-cache-dir flake8
 #  - pip install coverage # coveralls.io continuously monitors test case coverage
 #  - pip install coveralls
 ################

tests/ref_files/pq_example/code/Dockerfile

@@ -81,9 +81,9 @@ RUN conda install python=3.6 \
     && conda install -y r
 
 # Install python packages:
-RUN pip install --upgrade pip numpy setuptools \
-    && pip install cython \
-    && pip install pandas \
+RUN pip install --no-cache-dir --upgrade pip numpy setuptools \
+    && pip install --no-cache-dir cython \
+    && pip install --no-cache-dir pandas \
     && pip list
 
 # Install project specific packages:
@@ -117,7 +117,7 @@ RUN conda install -y r-docopt=0.4.5 r-data.table=1.10.4 r-ggplot2=2.2.1 ; \
 # Install package of interest
 ##############################
 
-RUN pip install git+git://github.com/EpiCompBio/stats_utils.git
+RUN pip install --no-cache-dir git+git://github.com/EpiCompBio/stats_utils.git
 
 ############################
 # Default action to start in

tests/ref_files/pq_example/code/pq_example/Dockerfile_pq_example_alpine

@@ -111,12 +111,12 @@ RUN conda update -y conda
 #    source deactivate'
 
 RUN conda install -y git ; \
-    pip install --upgrade pip cython numpy ; \
-    pip install pysam ; \
-    pip install pandas ; \
-    pip install ruffus ; \
+    pip install --no-cache-dir --upgrade pip cython numpy ; \
+    pip install --no-cache-dir pysam ; \
+    pip install --no-cache-dir pandas ; \
+    pip install --no-cache-dir ruffus ; \
     conda install sphinx ; \
-    pip install sphinxcontrib-bibtex ; \
+    pip install --no-cache-dir sphinxcontrib-bibtex ; \
     conda install -y -c r r=3.3 ; \
     conda install -y rpy2 ; \
     conda install -y readline ; \
@@ -127,15 +127,15 @@ RUN conda install -y git ; \
     conda install -y r-gdtools ; \
     R --vanilla -e 'source("https://bioconductor.org/biocLite.R") ; install.packages("svglite", repos = "http://cran.us.r-project.org") ; library("svglite")' ; \
     wget --no-check-certificate https://raw.githubusercontent.com/CGATOxford/cgat/master/requires.txt ; \
-    cat requires.txt | grep -v "#" | xargs -n 1 pip install ; \
+    cat requires.txt | grep -v "#" | xargs -n 1 pip install --no-cache-dir ; \
     conda install -y alignlib-lite ; \
     conda install -y bedtools ; \
     conda install -y pybedtools ; \
     conda install -y -c bioconda ucsc-wigtobigwig ; \
     conda install -y icu ; \
-    pip install git+git://github.com/AntonioJBT/CGATPipeline_core.git ; \
-    pip install git+git://github.com/AntonioJBT/project_quickstart.git ; \
-    pip install cgat 
+    pip install --no-cache-dir git+git://github.com/AntonioJBT/CGATPipeline_core.git ; \
+    pip install --no-cache-dir git+git://github.com/AntonioJBT/project_quickstart.git ; \
+    pip install --no-cache-dir cgat
 
 ############################
 # Default action to start in