Updated dependencies with pip-compile

docs/content/installation.rst

@@ -10,15 +10,14 @@ Remember -- deepTools are available for **command line usage** as well as for
 Requirements
 -------------
 
-* Python 2.7 or Python 3.x
-* numpy >= 1.8.0
-* scipy >= 0.17.0
-* py2bit >= 0.1.0
-* pyBigWig >= 0.2.1
-* pysam >= 0.8
-* matplotlib >= 1.4.0
-
-The fastest way to obtain **Python 2.7 or Python 3.x together with numpy and scipy** is
+* numpy
+* scipy
+* py2bit
+* pyBigWig
+* pysam
+* matplotlib
+
+The fastest way to obtain **Python together with numpy and scipy** is
 via the `Anaconda Scientific Python
 Distribution <https://store.continuum.io/cshop/anaconda/>`_.
 Just download the version that's suitable for your operating system and

docs/requirements.in

@@ -0,0 +1,4 @@
+numpydoc==0.6
+pysam
+sphinx-argparse
+deeptoolsintervals

docs/requirements.txt

@@ -1,4 +1,64 @@
+#
+# This file is autogenerated by pip-compile with python 3.9
+# To update, run:
+#
+#    pip-compile
+#
+alabaster==0.7.12
+    # via sphinx
+babel==2.10.1
+    # via sphinx
+certifi==2021.10.8
+    # via requests
+charset-normalizer==2.0.12
+    # via requests
+deeptoolsintervals==0.1.9
+    # via -r requirements.in
+docutils==0.17.1
+    # via sphinx
+idna==3.3
+    # via requests
+imagesize==1.3.0
+    # via sphinx
+importlib-metadata==4.11.3
+    # via sphinx
+jinja2==3.1.2
+    # via sphinx
+markupsafe==2.1.1
+    # via jinja2
 numpydoc==0.6
-pysam>=0.8.3
-sphinx-argparse
-deeptoolsintervals
+    # via -r requirements.in
+packaging==21.3
+    # via sphinx
+pygments==2.12.0
+    # via sphinx
+pyparsing==3.0.8
+    # via packaging
+pysam==0.19.0
+    # via -r requirements.in
+pytz==2022.1
+    # via babel
+requests==2.27.1
+    # via sphinx
+snowballstemmer==2.2.0
+    # via sphinx
+sphinx==4.5.0
+    # via sphinx-argparse
+sphinx-argparse==0.3.1
+    # via -r requirements.in
+sphinxcontrib-applehelp==1.0.2
+    # via sphinx
+sphinxcontrib-devhelp==1.0.2
+    # via sphinx
+sphinxcontrib-htmlhelp==2.0.0
+    # via sphinx
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==1.0.3
+    # via sphinx
+sphinxcontrib-serializinghtml==1.1.5
+    # via sphinx
+urllib3==1.26.9
+    # via requests
+zipp==3.8.0
+    # via importlib-metadata

galaxy/wrapper/plotHeatmap.xml

@@ -143,12 +143,13 @@
                 <param argument="--sortUsingSamples" type="text"
                     label="List of samples to be used for sorting"
                     help="List of sample numbers (order as in matrix), which are used by --sortUsing for sorting.
-                    If no value is set, it uses all samples. Example: 1 3 (space separated!)" />
+                    If no value is set, it uses all samples. Example: 1 3 (space separated!)">
                     <sanitizer>
                         <valid initial="string.printable">
                             <add value=" "/>
                         </valid>
-                    </sanitizer>
+                      </sanitizer>
+                    </param>
                 <param argument="--linesAtTickMarks" type="boolean" truevalue="--linesAtTickMarks" falsevalue=""
                     label="Draw dashed lines in heatmap above all tick marks?" />
                 <param argument="--averageTypeSummaryPlot" type="select"
@@ -246,12 +247,13 @@
                 <param argument="--clusterUsingSamples" type="text"
                     label="List of samples to be used for clustering"
                     help="List of sample numbers (order as in matrix), which are used by --kmeans or --hclust for clustering.
-                    If no value is set, it uses all samples. Example: 1 3 (space separated!)"/>
+                    If no value is set, it uses all samples. Example: 1 3 (space separated!)">
                     <sanitizer>
                         <valid initial="string.printable">
                             <add value=" "/>
                         </valid>
                     </sanitizer>
+                  </param>
             </when>
         </conditional>
     </inputs>

requirements.in

@@ -0,0 +1,9 @@
+numpy
+scipy
+matplotlib
+pysam
+py2bit
+numpydoc
+pyBigWig
+plotly
+deeptoolsintervals

requirements.txt

@@ -1,9 +1,99 @@
-numpy>=1.9.0
-scipy>=0.17.0
-matplotlib>=3.3.0
-pysam>=0.14.0
-py2bit>=0.2.0
-numpydoc>=0.5
-pyBigWig>=0.2.1
-plotly>=4.9
-deeptoolsintervals>=0.1.8
+#
+# This file is autogenerated by pip-compile with python 3.9
+# To update, run:
+#
+#    pip-compile
+#
+alabaster==0.7.12
+    # via sphinx
+babel==2.10.1
+    # via sphinx
+certifi==2021.10.8
+    # via requests
+charset-normalizer==2.0.12
+    # via requests
+cycler==0.11.0
+    # via matplotlib
+deeptoolsintervals==0.1.9
+    # via -r requirements.in
+docutils==0.17.1
+    # via sphinx
+fonttools==4.33.3
+    # via matplotlib
+idna==3.3
+    # via requests
+imagesize==1.3.0
+    # via sphinx
+importlib-metadata==4.11.3
+    # via sphinx
+jinja2==3.1.2
+    # via
+    #   numpydoc
+    #   sphinx
+kiwisolver==1.4.2
+    # via matplotlib
+markupsafe==2.1.1
+    # via jinja2
+matplotlib==3.5.2
+    # via -r requirements.in
+numpy==1.22.3
+    # via
+    #   -r requirements.in
+    #   matplotlib
+    #   scipy
+numpydoc==1.3.1
+    # via -r requirements.in
+packaging==21.3
+    # via
+    #   matplotlib
+    #   sphinx
+pillow==9.1.0
+    # via matplotlib
+plotly==5.7.0
+    # via -r requirements.in
+py2bit==0.3.0
+    # via -r requirements.in
+pybigwig==0.3.18
+    # via -r requirements.in
+pygments==2.12.0
+    # via sphinx
+pyparsing==3.0.8
+    # via
+    #   matplotlib
+    #   packaging
+pysam==0.19.0
+    # via -r requirements.in
+python-dateutil==2.8.2
+    # via matplotlib
+pytz==2022.1
+    # via babel
+requests==2.27.1
+    # via sphinx
+scipy==1.8.0
+    # via -r requirements.in
+six==1.16.0
+    # via
+    #   plotly
+    #   python-dateutil
+snowballstemmer==2.2.0
+    # via sphinx
+sphinx==4.5.0
+    # via numpydoc
+sphinxcontrib-applehelp==1.0.2
+    # via sphinx
+sphinxcontrib-devhelp==1.0.2
+    # via sphinx
+sphinxcontrib-htmlhelp==2.0.0
+    # via sphinx
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==1.0.3
+    # via sphinx
+sphinxcontrib-serializinghtml==1.1.5
+    # via sphinx
+tenacity==8.0.1
+    # via plotly
+urllib3==1.26.9
+    # via requests
+zipp==3.8.0
+    # via importlib-metadata