Repository: bioconvert/bioconvert (language: python)

Issue:
naming of requirement_tools is ambiguous (should be merged with environment.yml)
- requirements.txt is the list of Python deps to be found on pypi
- requirements_dev.txt is the list of Python deps for developers to be found on pypi (e.g pytest sphinx, etc)
- requirements_tools.txt contains all conda dependencies **This is not standard naming**. should be renamed in environment.yml, which already exists. So the content of requirements_tools.txt should be merged into enrironment.yml and requirements_tools.txt deleted


Discussion / hints:

Fix patch:
diff --git a/.github/workflows/bam2sam.yml b/.github/workflows/bam2sam.yml
index d4164215..013b607b 100644
--- a/.github/workflows/bam2sam.yml
+++ b/.github/workflows/bam2sam.yml
@@ -51,4 +51,4 @@ jobs:
         pip install .
     - name: Test with pytest
       run: |
-        pytest -n 1  --cov-report term --cov=bioconvert.bam2sam test/test_bam2sam.py
\ No newline at end of file
+        pytest -n 1  --cov-report term --cov=bioconvert.bam2sam test/test_bam2sam.py
diff --git a/.github/workflows/fastq2fasta.yml b/.github/workflows/fastq2fasta.yml
index 136a8288..e3c31a1d 100644
--- a/.github/workflows/fastq2fasta.yml
+++ b/.github/workflows/fastq2fasta.yml
@@ -51,4 +51,4 @@ jobs:
         pip install .
     - name: Test with pytest
       run: |
-        pytest -n 1  --cov-report term --cov=bioconvert.fastq2fasta test/test_fastq2fasta.py
\ No newline at end of file
+        pytest -n 1  --cov-report term --cov=bioconvert.fastq2fasta test/test_fastq2fasta.py
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 25304f3d..00000000
--- a/.travis.yml
+++ /dev/null
@@ -1,76 +0,0 @@
-language: python
-
-cache:
-  directories:
-    - $HOME/.cache/pip
-
-matrix:
-  include:
-    - name: linux Python 3.5
-      os: linux
-      sudo: required
-      python: 3.5
-    - name: Linux Python 3.6
-      os: linux
-      sudo: required
-      python: 3.6
-
-services:
-  - xvfb
-
-branches:
-  only:
-    - master
-    - dev
-    - osxtest
-
-# solution based on https://gist.github.com/dan-blanchard/7045057
-# setup anaconda to install scipy and numpy easily and quickly
-before_install:
-    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh; else wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi
-    - chmod +x miniconda.sh
-    - ./miniconda.sh -b
-    - export PATH=$HOME/miniconda3/bin:$PATH
-    - hash -r
-    - conda update --yes conda
-    - conda config --add channels r
-    - conda config --add channels defaults
-    - conda config --add channels conda-forge
-    - conda config --add channels bioconda
-    # are not specific to using mini
-    #- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo rm -rf /dev/shm; fi
-    #- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ln -s /run/shm /dev/shm; fi
-    # This help testing code with pylab
-    #- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export DISPLAY=:99.0; fi
-    #- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sh -e /etc/init.d/xvfb start; fi
-
-install:
-  - echo $TRAVIS_PYTHON_VERSION
-  - conda create --yes --name testenv python=$TRAVIS_PYTHON_VERSION
-  - source activate testenv
-
-  - conda install --yes --file requirements.txt
-  - conda install --yes --file requirements_tools.txt
-  - conda install --yes --file requirements_dev.txt
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then conda install --yes --file requirements_tools_linux_only.txt;  fi
-  - conda install --yes  coverage
-  # Issue on 24th May 2019 telling RuntimeError: module compiled against API YY
-  # version but this version of numpy is XX when using pyBigWig
-  #- conda install --yes numpy pyBigWig
-  - pip install .
-  #- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then pip install pygatb --no-deps ; fi
-  - pip install pypandoc
-  - pip install biocode
-
-  # May 11 2019, error on travis in osx https://github.com/MTG/sms-tools/issues/36
-  #- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; mkdir -p ~/.matplotlib; echo "backend: TkAgg" > ~/.matplotlib/matplotlibrc
-
-
-
-# # command to run tests, e.g. python setup.py test
-script:
-  - pytest -v --durations=10  test/ --cov=bioconvert --cov-report term --timeout 300 -n 1
-
-
-after_success:
-  coveralls
diff --git a/README.rst b/README.rst
index 4bd3d703..8d590583 100644
--- a/README.rst
+++ b/README.rst
@@ -222,4 +222,16 @@ Setting up and maintaining Bioconvert has been possible thanks to users and cont
 Thanks to all:
 
 .. image:: https://contrib.rocks/image?repo=bioconvert/bioconvert
-    :target: https://github.com/bioconvert/bioconvert/graphs/contributors
\ No newline at end of file
+    :target: https://github.com/bioconvert/bioconvert/graphs/contributors
+
+
+Changes
+########
+
+========= ====================================================================
+Version   Description
+========= ====================================================================
+0.5.0     * Add CI actions for all converters
+          * remove sniffer (now in biosniff)
+========= ====================================================================
+
diff --git a/environment.yml b/environment.yml
index ba390018..276ab007 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,11 +1,39 @@
-name: py36-bioconvert
+name: bioconvert
+
 channels:
-  - bioconda
-  - conda-forge
-  - defaults
-  - r
+- bioconda
+- conda-forge
+- defaults
+- r
+
 dependencies:
-  - bioconvert
-  - mosdepth
-  - perl
-  - python=3.6
+- python=3.7
+- bedtools
+- biopython
+- bioawk
+- colorlog
+- biopython
+- numpy
+- matplotlib
+- pandas
+- pyBigWig
+- mawk
+- scipy
+- pysam
+- pillow
+- easydev
+- plink
+- pyyaml
+- pillow
+- singularity
+- pigz
+- dsrc
+- sambamba
+- seqtk
+- seqkit
+- wiggletools
+- graphviz   # provides dot for RTD
+- ucsc-wigtobigwig
+- ucsc-twobittofa
+- ucsc-fatotwobit
+- ucsc-bigwigtobedgraph
diff --git a/environment_rtd.yml b/environment_rtd.yml
index c8abde6f..2d2180d4 100644
--- a/environment_rtd.yml
+++ b/environment_rtd.yml
@@ -8,12 +8,16 @@ channels:
 
 dependencies:
 - python=3.7
+- bedtools
+- biopython
+- bioawk
 - colorlog
 - biopython
 - numpy
 - matplotlib
 - pandas
 - pyBigWig
+- mawk
 - scipy
 - pysam
 - pillow
@@ -21,17 +25,17 @@ dependencies:
 - pip
 - pyyaml
 - pillow
-- bedtools          # used in gallery and bam2bed
 - singularity
 - pigz
 - dsrc
 - sambamba
-- bioawk
 - seqtk
 - seqkit
+- wiggletools
 - graphviz   # provides dot for RTD
 - icu
 
+
 - pip:
   - docutils<0.13.1 # https://github.com/sphinx-doc/sphinx/issues/3212
   - pyexcel
diff --git a/requirements_tools.txt b/requirements_tools.txt
deleted file mode 100644
index 31297566..00000000
--- a/requirements_tools.txt
+++ /dev/null
@@ -1,22 +0,0 @@
-bamtools
-bcftools==1.8
-bedops
-bedtools
-go=1.10.3
-pbzip2
-pigz
-plink
-samtools>=1.9
-seqtk
-squizz
-sra-tools
-ucsc-bedgraphtobigwig
-ucsc-bigwigtobedgraph
-ucsc-fatotwobit
-ucsc-twobittofa
-wiggletools>=1.2.2
-sed
-mawk
-dsrc
-sambamba
-deeptools
diff --git a/requirements_tools_linux_only.txt b/requirements_tools_linux_only.txt
deleted file mode 100644
index d62bfacc..00000000
--- a/requirements_tools_linux_only.txt
+++ /dev/null
@@ -1,1 +0,0 @@
-mosdepth
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 685aab3b..78ef8327 100755
--- a/setup.py
+++ b/setup.py
@@ -80,10 +80,8 @@
     entry_points={
         'console_scripts': [
            'bioconvert=bioconvert.scripts.converter:main',
-           #'proto_sub_cmd=bioconvert.scripts.proto_sub_cmd:main',
            'bioconvert_init=bioconvert.scripts.init_convert:main',
            'bioconvert_stats=bioconvert.scripts.stats:main',
-           'bioconvert_sniffer=bioconvert.scripts.sniffer:main'
         ]
     }
     )


Test patch:
diff --git a/bioconvert/data/test_bcf2vcf_v1.bcf.csi b/bioconvert/data/test_bcf2vcf_v1.bcf.csi
new file mode 100644
index 00000000..38e3aaa1
Binary files /dev/null and b/bioconvert/data/test_bcf2vcf_v1.bcf.csi differ
diff --git a/bioconvert/data/test_bcf2wiggle.wiggle b/bioconvert/data/test_bcf2wiggle.wiggle
index c478d438..104e13b3 100644
--- a/bioconvert/data/test_bcf2wiggle.wiggle
+++ b/bioconvert/data/test_bcf2wiggle.wiggle
@@ -1,166 +1,83 @@
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