Adding tests and configuring tox.ini

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v2

requirements/base.in

@@ -0,0 +1,21 @@
+bioconda2biocontainer
+biopython
+cookiecutter
+cwltool
+docker
+galaxy-tool-util
+GitPython
+goenrichment
+jupyter
+matplotlib
+networkx
+numpy
+pandas
+pdf2image
+PyYAML
+requests
+scipy
+seaborn
+statsmodels
+urllib3
+xmltodict

requirements/base.txt

@@ -1,21 +1,128 @@
-bioconda2biocontainer~=0.0.3
-biopython~=1.77
-cookiecutter~=1.7.2
-cwltool~=3.0.20200710214758
-docker~=4.2.2
-galaxy-tool-util~=20.5.0
-GitPython~=3.1.7
-goenrichment~=0.0.10a3
-jupyter~=1.0.0
-matplotlib~=3.3.0
-networkx~=2.4
-numpy~=1.19.0
-pandas~=1.0.5
-pdf2image~=1.13.1
-PyYAML~=5.3.1
-requests~=2.24.0
-scipy~=1.5.1
-seaborn~=0.10.1
-statsmodels~=0.11.1
-urllib3~=1.25.9
-xmltodict~=0.12.0
+# SHA1:2016d815aabb3e67f3ea04ab7fed4def6fbdf0bf
+#
+# This file is autogenerated by pip-compile-multi
+# To update, run:
+#
+#    pip-compile-multi
+#
+appnope==0.1.0            # via ipykernel, ipython
+argon2-cffi==20.1.0       # via notebook
+arrow==0.16.0             # via jinja2-time
+async-generator==1.10     # via nbclient
+attrs==20.2.0             # via jsonschema
+backcall==0.2.0           # via ipython
+bagit==1.7.0              # via cwltool
+binaryornot==0.4.4        # via cookiecutter
+bioconda2biocontainer==0.0.4  # via -r requirements/base.in
+biopython==1.78           # via -r requirements/base.in
+bleach==3.2.0             # via galaxy-util, nbconvert
+boltons==20.2.1           # via galaxy-util
+cachecontrol==0.11.7      # via schema-salad
+certifi==2020.6.20        # via matplotlib, requests
+cffi==1.14.2              # via argon2-cffi
+chardet==3.0.4            # via binaryornot, requests
+click==7.1.2              # via cookiecutter
+coloredlogs==14.0         # via cwltool
+cookiecutter==1.7.2       # via -r requirements/base.in
+cwltool==3.0.20200807132242  # via -r requirements/base.in
+cycler==0.10.0            # via matplotlib
+decorator==4.4.2          # via ipython, networkx
+defusedxml==0.6.0         # via nbconvert
+docker==4.3.1             # via -r requirements/base.in
+docutils==0.16            # via galaxy-util
+entrypoints==0.3          # via nbconvert
+galaxy-containers==20.5.0  # via galaxy-tool-util
+galaxy-tool-util==20.5.0  # via -r requirements/base.in
+galaxy-util==20.5.0       # via galaxy-containers, galaxy-tool-util
+gitdb==4.0.5              # via gitpython
+gitpython==3.1.8          # via -r requirements/base.in
+goenrichment==0.0.10a3    # via -r requirements/base.in
+humanfriendly==8.2        # via coloredlogs
+idna==2.10                # via requests
+importlib-metadata==1.7.0  # via jsonschema
+ipykernel==5.3.4          # via ipywidgets, jupyter, jupyter-console, notebook, qtconsole
+ipython-genutils==0.2.0   # via nbformat, notebook, qtconsole, traitlets
+ipython==7.18.1           # via ipykernel, ipywidgets, jupyter-console
+ipywidgets==7.5.1         # via jupyter
+isodate==0.6.0            # via rdflib
+jedi==0.17.2              # via ipython
+jinja2-time==0.2.0        # via cookiecutter
+jinja2==2.11.2            # via cookiecutter, jinja2-time, nbconvert, notebook
+jsonschema==3.2.0         # via nbformat
+jupyter-client==6.1.7     # via ipykernel, jupyter-console, nbclient, notebook, qtconsole
+jupyter-console==6.2.0    # via jupyter
+jupyter-core==4.6.3       # via jupyter-client, nbconvert, nbformat, notebook, qtconsole
+jupyter==1.0.0            # via -r requirements/base.in
+jupyterlab-pygments==0.1.1  # via nbconvert
+kiwisolver==1.2.0         # via matplotlib
+lockfile==0.12.2          # via schema-salad
+lxml==4.5.2               # via prov
+markupsafe==1.1.1         # via cookiecutter, galaxy-util, jinja2
+matplotlib==3.3.2         # via -r requirements/base.in, seaborn
+mistune==0.8.4            # via nbconvert, schema-salad
+mypy-extensions==0.4.3    # via cwltool
+nbclient==0.5.0           # via nbconvert
+nbconvert==6.0.3          # via jupyter, notebook
+nbformat==5.0.7           # via ipywidgets, nbclient, nbconvert, notebook
+nest-asyncio==1.4.0       # via nbclient
+networkx==2.5             # via -r requirements/base.in, goenrichment, prov
+notebook==6.1.4           # via jupyter, widgetsnbextension
+numpy==1.19.2             # via -r requirements/base.in, biopython, goenrichment, matplotlib, pandas, patsy, scipy, seaborn, statsmodels
+packaging==20.4           # via bleach, galaxy-util
+pandas==1.1.2             # via -r requirements/base.in, goenrichment, seaborn, statsmodels
+pandocfilters==1.4.2      # via nbconvert
+parso==0.7.1              # via jedi
+patsy==0.5.1              # via statsmodels
+pdf2image==1.14.0         # via -r requirements/base.in
+pexpect==4.8.0            # via ipython
+pickleshare==0.7.5        # via ipython
+pillow==7.2.0             # via matplotlib, pdf2image
+poyo==0.5.0               # via cookiecutter
+prometheus-client==0.8.0  # via notebook
+prompt-toolkit==3.0.7     # via ipython, jupyter-console
+prov==1.5.1               # via cwltool
+psutil==5.7.2             # via cwltool
+ptyprocess==0.6.0         # via pexpect, terminado
+pycparser==2.20           # via cffi
+pydot==1.4.1              # via cwltool
+pygments==2.7.1           # via ipython, jupyter-console, jupyterlab-pygments, nbconvert, qtconsole
+pyparsing==2.4.7          # via matplotlib, packaging, pydot, rdflib
+pyrsistent==0.17.3        # via jsonschema
+python-dateutil==2.8.1    # via arrow, jupyter-client, matplotlib, pandas, prov
+python-slugify==4.0.1     # via cookiecutter
+pytz==2020.1              # via pandas
+pyyaml==5.3.1             # via -r requirements/base.in, bioconda2biocontainer, galaxy-util
+pyzmq==19.0.2             # via jupyter-client, notebook, qtconsole
+qtconsole==4.7.7          # via jupyter
+qtpy==1.9.0               # via qtconsole
+rdflib-jsonld==0.5.0      # via schema-salad
+rdflib==4.2.2             # via cwltool, prov, rdflib-jsonld, schema-salad
+repoze.lru==0.7           # via routes
+requests==2.24.0          # via -r requirements/base.in, bioconda2biocontainer, cachecontrol, cookiecutter, cwltool, docker, galaxy-containers, galaxy-util, schema-salad
+routes==2.4.1             # via galaxy-util
+ruamel.yaml.clib==0.2.2   # via ruamel.yaml
+ruamel.yaml==0.16.5       # via cwltool, schema-salad
+schema-salad==7.0.20200811075006  # via cwltool
+scipy==1.5.2              # via -r requirements/base.in, goenrichment, seaborn, statsmodels
+seaborn==0.11.0           # via -r requirements/base.in
+send2trash==1.5.0         # via notebook
+shellescape==3.4.1        # via cwltool
+six==1.15.0               # via argon2-cffi, bleach, cookiecutter, cycler, docker, galaxy-util, isodate, jsonschema, packaging, patsy, prov, python-dateutil, routes, websocket-client
+smmap==3.0.4              # via gitdb
+statsmodels==0.12.0       # via -r requirements/base.in, goenrichment
+terminado==0.8.3          # via notebook
+testpath==0.4.4           # via nbconvert
+text-unidecode==1.3       # via python-slugify
+tornado==6.0.4            # via ipykernel, jupyter-client, notebook, terminado
+traitlets==5.0.4          # via ipykernel, ipython, ipywidgets, jupyter-client, jupyter-core, nbclient, nbconvert, nbformat, notebook, qtconsole
+typing-extensions==3.7.4.3  # via cwltool, schema-salad
+urllib3==1.25.10          # via -r requirements/base.in, requests
+wcwidth==0.2.5            # via prompt-toolkit
+webencodings==0.5.1       # via bleach
+websocket-client==0.57.0  # via docker
+widgetsnbextension==3.5.1  # via ipywidgets
+xmltodict==0.12.0         # via -r requirements/base.in
+zipp==3.1.0               # via importlib-metadata
+
+# The following packages are considered to be unsafe in a requirements file:
+# setuptools

requirements/test.in

@@ -0,0 +1,8 @@
+-r base.txt
+
+pytest
+pytest-cov
+sphinx-argparse
+mock
+sphinx-rtd-theme
+

requirements/test.txt

@@ -1,4 +1,33 @@
+# SHA1:6d4c9a6ffab8b2fa46a52aa17b0c622b8bdf93cd
+#
+# This file is autogenerated by pip-compile-multi
+# To update, run:
+#
+#    pip-compile-multi
+#
 -r base.txt
+alabaster==0.7.12         # via sphinx
+babel==2.8.0              # via sphinx
+coverage==5.3             # via pytest-cov
+imagesize==1.2.0          # via sphinx
+iniconfig==1.0.1          # via pytest
+mock==4.0.2               # via -r requirements/test.in
+more-itertools==8.5.0     # via pytest
+pluggy==0.13.1            # via pytest
+py==1.9.0                 # via pytest
+pytest-cov==2.10.1        # via -r requirements/test.in
+pytest==6.0.2             # via -r requirements/test.in, pytest-cov
+snowballstemmer==2.0.0    # via sphinx
+sphinx-argparse==0.2.5    # via -r requirements/test.in
+sphinx-rtd-theme==0.5.0   # via -r requirements/test.in
+sphinx==3.2.1             # via sphinx-argparse, sphinx-rtd-theme
+sphinxcontrib-applehelp==1.0.2  # via sphinx
+sphinxcontrib-devhelp==1.0.2  # via sphinx
+sphinxcontrib-htmlhelp==1.0.3  # via sphinx
+sphinxcontrib-jsmath==1.0.1  # via sphinx
+sphinxcontrib-qthelp==1.0.3  # via sphinx
+sphinxcontrib-serializinghtml==1.1.4  # via sphinx
+toml==0.10.1              # via pytest
 
-pytest~=3.7
-pytest-cov~=2.5
+# The following packages are considered to be unsafe in a requirements file:
+# setuptools

setup.py

@@ -53,16 +53,12 @@ def readme():
                       'Wand',
                       'xmltodict'],
     classifiers=[
-        'Development Status :: 3 - Alpha',
+        'Development Status :: 4 - Beta',
         'Intended Audience :: Science/Research',
         'License :: Public Domain',
         'Natural Language :: English',
         'Operating System :: Unix',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.3',
-        'Programming Language :: Python :: 3.4',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Topic :: Scientific/Engineering :: Bio-Informatics'

src/pm4ngs/cookiecutter.py

@@ -26,6 +26,6 @@ def execute_cookiecutter(template, config_file, sample_table, copy_rawdata):
                          no_input=no_input,
                          extra_context=extra_context['default_context'])
         except FailedHookException as e:
-            print()
+            print(e)
     else:
         print('Sample table file {} not found.'.format(sample_table))

src/pm4ngs/jupyterngsplugin/markdown/chipexo.py

@@ -1,8 +1,10 @@
 import os
+
 import pandas
+
 from pm4ngs.jupyterngsplugin.markdown.utils import get_link_image
-from pm4ngs.jupyterngsplugin.utils.count_lines import count_lines
 from pm4ngs.jupyterngsplugin.markdown.utils import get_link_text
+from pm4ngs.jupyterngsplugin.utils.count_lines import count_lines
 
 
 def peak_calling_table_with_qc(factors, alignment_path, peak_calling_path, width, height):
@@ -57,6 +59,55 @@ def peak_calling_table_with_qc(factors, alignment_path, peak_calling_path, width
     return str_msg
 
 
+def meme_motif_table_condition(motif_path, c, d, width, height):
+    str_msg = ''
+    f = os.path.relpath(os.path.join(motif_path, c + '.border_pair_annot_' + d,
+                                     'summary.tsv'))
+    if os.path.exists(f) and os.path.getsize(f) != 0:
+        df = pandas.read_csv(f, sep='\t', comment='#')
+        if not df.empty:
+            n_motif = len(df)
+            source = df.iloc[0]['MOTIF_SOURCE']
+            consensus = df.iloc[0]['CONSENSUS']
+            w = df.iloc[0]['WIDTH']
+            sites = df.iloc[0]['SITES']
+            e_value = df.iloc[0]['E-VALUE']
+            lhtml = os.path.relpath(os.path.join(motif_path, c + '.border_pair_annot_' + d,
+                                                 'meme-chip.html'))
+            str_msg += '| ' + get_link_text(lhtml, c, ' --- ')
+            str_msg += '|'
+
+            str_msg += " {} | {} | {} | {} | {} | {} | ".format(n_motif, source, consensus,
+                                                                w, sites, e_value)
+            if source == 'MEME':
+                lpng = os.path.relpath(
+                    os.path.join(motif_path, c + '.border_pair_annot_' + d, 'meme_out',
+                                 'logo1.png'))
+                if os.path.exists(lpng) and os.path.getsize(lpng) != 0:
+                    str_msg += get_link_image(lpng, width, height, ' --- ')
+                    str_msg += ' |'
+                else:
+                    str_msg += ' --- |'
+            elif source == 'DREME':
+                lout = os.path.relpath(os.path.join(motif_path, c
+                                                    + '.border_pair_annot_'
+                                                    + d,
+                                                    'dreme_out'))
+                dreme_files = [f for ds, dr, files in os.walk(lout)
+                               for f in files if f.startswith('m01nc')]
+                for dm in dreme_files:
+                    loutfile = os.path.relpath(
+                        os.path.join(motif_path, c + '.border_pair_annot_' + d,
+                                     'dreme_out', dm))
+                    if os.path.exists(loutfile) and os.path.getsize(loutfile) != 0:
+                        str_msg += get_link_image(loutfile, width, height, ' --- ')
+                        str_msg += ' |'
+                    else:
+                        str_msg += ' --- |'
+            str_msg += '\n'
+    return str_msg
+
+
 def meme_motif_table(factors, motif_path, width, height):
     """
     Create a table for the MEME motif find results
@@ -68,7 +119,7 @@ def meme_motif_table(factors, motif_path, width, height):
     """
     conditions = factors['condition'].unique()
     memedbs = []
-    dirs = [ d for d in os.listdir(motif_path) if os.path.isdir(os.path.join(motif_path, d))]
+    dirs = [d for d in os.listdir(motif_path) if os.path.isdir(os.path.join(motif_path, d))]
     for d in dirs:
         if '.border_pair_annot_' in d:
             d = d.split('.border_pair_annot_')[1]
@@ -82,47 +133,6 @@ def meme_motif_table(factors, motif_path, width, height):
         str_msg += "| 1st motif<br>E-Value | 1st motif |\n"
         str_msg += "| --- | --- | --- | --- | --- | --- | --- | --- |\n"
         for c in conditions:
-            f = os.path.relpath(os.path.join(motif_path, c + '.border_pair_annot_' + d,
-                                             'summary.tsv'))
-            if os.path.exists(f) and os.path.getsize(f) != 0:
-                df = pandas.read_csv(f, sep='\t', comment='#')
-                if not df.empty:
-                    n_motif = len(df)
-                    source = df.iloc[0]['MOTIF_SOURCE']
-                    consensus = df.iloc[0]['CONSENSUS']
-                    w = df.iloc[0]['WIDTH']
-                    sites = df.iloc[0]['SITES']
-                    e_value = df.iloc[0]['E-VALUE']
-                    lhtml = os.path.relpath(os.path.join(motif_path, c + '.border_pair_annot_' + d,
-                                                         'meme-chip.html'))
-                    str_msg += '| ' + get_link_text(lhtml, c, ' --- ')
-                    str_msg += '|'
-
-                    str_msg += " {} | {} | {} | {} | {} | {} | ".format(n_motif, source, consensus,
-                                                                        w, sites, e_value)
-                    if source == 'MEME':
-                        lpng = os.path.relpath(
-                            os.path.join(motif_path, c + '.border_pair_annot_' + d, 'meme_out',
-                                         'logo1.png'))
-                        if os.path.exists(lpng) and os.path.getsize(lpng) != 0:
-                            str_msg += get_link_image(lpng, width, height, ' --- ')
-                            str_msg += ' |'
-                        else:
-                            str_msg += ' --- |'
-                    elif source == 'DREME':
-                        lout = os.path.relpath(os.path.join(motif_path, c + '.border_pair_annot_' + d,
-                                                            'dreme_out'))
-                        dreme_files = [f for ds, dr, files in os.walk(lout)
-                                       for f in files if f.startswith('m01nc')]
-                        for dm in dreme_files:
-                            loutfile = os.path.relpath(
-                                os.path.join(motif_path, c + '.border_pair_annot_' + d,
-                                             'dreme_out', dm))
-                            if os.path.exists(loutfile) and os.path.getsize(loutfile) != 0:
-                                str_msg += get_link_image(loutfile, width, height, ' --- ')
-                                str_msg += ' |'
-                            else:
-                                str_msg += ' --- |'
-                    str_msg += '\n'
+            str_msg += meme_motif_table_condition(motif_path, c, d, width, height)
         str_msg += '\n\n\n'
     return str_msg