Merge pull request #1277 from deeptools/docs_pyreqs

Docs pyreqs

.github/workflows/test.yml

@@ -73,7 +73,7 @@ jobs:
     needs: build-linux
     strategy:
       matrix:
-        python-version: ['3.7','3.8','3.9','3.10', '3.11']
+        python-version: ['3.8','3.9','3.10', '3.11', '3.12']
     steps:
       - uses: actions/checkout@v3
       - uses: actions/download-artifact@v3

.readthedocs.yaml

@@ -3,11 +3,13 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.12"
 
 sphinx:
   configuration: docs/conf.py
 
 python:
   install:
+  - method: pip
+    path: .
   - requirements: docs/requirements.txt

README.md

@@ -4,7 +4,6 @@
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/deeptools/README.html)
 [![European Galaxy server](https://img.shields.io/badge/usegalaxy-.eu-brightgreen?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABgAAAASCAYAAABB7B6eAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAACXBIWXMAAAsTAAALEwEAmpwYAAACC2lUWHRYTUw6Y29tLmFkb2JlLnhtcAAAAAAAPHg6eG1wbWV0YSB4bWxuczp4PSJhZG9iZTpuczptZXRhLyIgeDp4bXB0az0iWE1QIENvcmUgNS40LjAiPgogICA8cmRmOlJERiB4bWxuczpyZGY9Imh0dHA6Ly93d3cudzMub3JnLzE5OTkvMDIvMjItcmRmLXN5bnRheC1ucyMiPgogICAgICA8cmRmOkRlc2NyaXB0aW9uIHJkZjphYm91dD0iIgogICAgICAgICAgICB4bWxuczp0aWZmPSJodHRwOi8vbnMuYWRvYmUuY29tL3RpZmYvMS4wLyI+CiAgICAgICAgIDx0aWZmOlJlc29sdXRpb25Vbml0PjI8L3RpZmY6UmVzb2x1dGlvblVuaXQ+CiAgICAgICAgIDx0aWZmOkNvbXByZXNzaW9uPjE8L3RpZmY6Q29tcHJlc3Npb24+CiAgICAgICAgIDx0aWZmOk9yaWVudGF0aW9uPjE8L3RpZmY6T3JpZW50YXRpb24+CiAgICAgICAgIDx0aWZmOlBob3RvbWV0cmljSW50ZXJwcmV0YXRpb24+MjwvdGlmZjpQaG90b21ldHJpY0ludGVycHJldGF0aW9uPgogICAgICA8L3JkZjpEZXNjcmlwdGlvbj4KICAgPC9yZGY6UkRGPgo8L3g6eG1wbWV0YT4KD0UqkwAAAn9JREFUOBGlVEuLE0EQruqZiftwDz4QYT1IYM8eFkHFw/4HYX+GB3/B4l/YP+CP8OBNTwpCwFMQXAQPKtnsg5nJZpKdni6/6kzHvAYDFtRUT71f3UwAEbkLch9ogQxcBwRKMfAnM1/CBwgrbxkgPAYqlBOy1jfovlaPsEiWPROZmqmZKKzOYCJb/AbdYLso9/9B6GppBRqCrjSYYaquZq20EUKAzVpjo1FzWRDVrNay6C/HDxT92wXrAVCH3ASqq5VqEtv1WZ13Mdwf8LFyyKECNbgHHAObWhScf4Wnj9CbQpPzWYU3UFoX3qkhlG8AY2BTQt5/EA7qaEPQsgGLWied0A8VKrHAsCC1eJ6EFoUd1v6GoPOaRAtDPViUr/wPzkIFV9AaAZGtYB568VyJfijV+ZBzlVZJ3W7XHB2RESGe4opXIGzRTdjcAupOK09RA6kzr1NTrTj7V1ugM4VgPGWEw+e39CxO6JUw5XhhKihmaDacU2GiR0Ohcc4cZ+Kq3AjlEnEeRSazLs6/9b/kh4eTC+hngE3QQD7Yyclxsrf3cpxsPXn+cFdenF9aqlBXMXaDiEyfyfawBz2RqC/O9WF1ysacOpytlUSoqNrtfbS642+4D4CS9V3xb4u8P/ACI4O810efRu6KsC0QnjHJGaq4IOGUjWTo/YDZDB3xSIxcGyNlWcTucb4T3in/3IaueNrZyX0lGOrWndstOr+w21UlVFokILjJLFhPukbVY8OmwNQ3nZgNJNmKDccusSb4UIe+gtkI+9/bSLJDjqn763f5CQ5TLApmICkqwR0QnUPKZFIUnoozWcQuRbC0Km02knj0tPYx63furGs3x/iPnz83zJDVNtdP3QAAAABJRU5ErkJggg==)](https://usegalaxy.eu/root?tool_id=deeptools_compute_matrix)
 ![test](https://github.com/deeptools/deepTools/actions/workflows/test.yml/badge.svg)
-![planemo](https://github.com/deeptools/deepTools/actions/workflows/planemo.yml/badge.svg)
 
 
 ## User-friendly tools for exploring deep-sequencing data
@@ -34,35 +33,26 @@ Our [Gallery](http://deeptools.readthedocs.org/en/latest/content/example_gallery
 
 deepTools are available for:
 
-* Command line usage (via pip/anaconda/github)
+* Command line usage (via pip / conda / github)
 * Integration into Galaxy servers (via toolshed/API/web-browser)
 
-There are many easy ways to install deepTools. Details can be found [here](https://deeptools.readthedocs.io/en/latest/content/installation.html)
+There are many easy ways to install deepTools. More details can be found [here](https://deeptools.readthedocs.io/en/latest/content/installation.html).
 
-**Install by cloning this repository:**
+In Brief:
 
-You can install any one of the deepTools branches on command line (linux/mac) by cloning this git repository :
+**Install through pypi**
 
-	$ git clone https://github.com/deeptools/deepTools
-	$ cd deepTools
-	$ python setup.py install
-
-By default, the script will install the python library and executable
-codes globally, which means you need to be root or administrator of
-the machine to complete the installation. If you need to
-provide a nonstandard install prefix, or any other nonstandard
-options, you can provide many command line options to the install
-script.
+	$ pip install deeptools
 
-	$ python setup.py --help
+**Install via conda**
 
-For example, to install under a specific location use:
+	$ conda install -c bioconda deeptools
 
-	$ python setup.py install --prefix <target directory>
+**Install by cloning the repository**
 
-To install into your home directory, use:
-
-	$ python setup.py install --user
+	$ git clone https://github.com/deeptools/deepTools
+	$ cd deepTools
+	$ pip install .
 
 <a name="galaxy"/></a>
 ### Galaxy Installation

deeptools/alignmentSieve.py

@@ -7,11 +7,8 @@
 from deeptools import parserCommon
 from deeptools.bamHandler import openBam
 from deeptools.mapReduce import mapReduce
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
 from deeptools.utilities import getTLen, smartLabels, getTempFileName
+from importlib.metadata import version
 
 
 def parseArguments():

deeptools/bamPEFragmentSize.py

@@ -18,10 +18,7 @@
 # own tools
 from deeptools.parserCommon import writableFile
 from deeptools.getFragmentAndReadSize import get_read_and_fragment_length
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
+from importlib.metadata import version
 
 
 def parse_arguments():

deeptools/computeMatrix.py

@@ -7,14 +7,11 @@
 import multiprocessing
 
 from deeptools.parserCommon import writableFile, numberOfProcessors
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
 from deeptools import parserCommon
 from deeptools import heatmapper
 import deeptools.computeMatrixOperations as cmo
 import deeptools.deepBlue as db
+from importlib.metadata import version
 
 
 def parse_arguments(args=None):

deeptools/computeMatrixOperations.py

@@ -6,10 +6,7 @@
 import sys
 import os
 import csv
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
+from importlib.metadata import version
 
 
 def parse_arguments():

deeptools/deeptools_list_tools.py

@@ -3,10 +3,7 @@
 
 import argparse
 import sys
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
+from importlib.metadata import version
 
 
 def parse_arguments(args=None):

deeptools/estimateReadFiltering.py

@@ -5,10 +5,7 @@
 from deeptools import parserCommon, bamHandler, utilities
 from deeptools.mapReduce import mapReduce
 from deeptools.utilities import smartLabels
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
+from importlib.metadata import version
 
 
 def parseArguments():

deeptools/estimateScaleFactor.py

@@ -6,11 +6,7 @@
 
 from deeptools.SES_scaleFactor import estimateScaleFactor
 from deeptools.parserCommon import numberOfProcessors
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
-
+from importlib.metadata import version
 debug = 0
 
 

deeptools/getFragmentAndReadSize.py

@@ -76,7 +76,8 @@ def get_read_and_fragment_length(bamFile, return_lengths=False, blackListFileNam
     -------
     d : dict
         tuple of two dictionaries, one for the fragment length and the other
-        for the read length. The dictionaries summarise the mean, median etc. values
+for the read length. The dictionaries summarise the mean, median etc. values
+
     """
 
     bam_handle = bamHandler.openBam(bamFile)

deeptools/multiBamSummary.py

@@ -9,11 +9,7 @@
 import deeptools.countReadsPerBin as countR
 from deeptools import parserCommon
 from deeptools.utilities import smartLabels
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
-
+from importlib.metadata import version
 old_settings = np.seterr(all='ignore')
 
 

deeptools/multiBigwigSummary.py

@@ -10,10 +10,7 @@
 from deeptools.utilities import smartLabels
 import deeptools.getScorePerBigWigBin as score_bw
 import deeptools.deepBlue as db
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
+from importlib.metadata import version
 
 old_settings = np.seterr(all='ignore')
 

deeptools/parserCommon.py

@@ -1,9 +1,6 @@
 import argparse
 import os
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
+from importlib.metadata import version
 
 
 def check_float_0_1(value):

deeptools/plotCorrelation.py

@@ -10,13 +10,9 @@
 matplotlib.rcParams['svg.fonttype'] = 'none'
 from deeptools import cm  # noqa: F401
 import matplotlib.pyplot as plt
-
+from importlib.metadata import version
 from deeptools.correlation import Correlation
 from deeptools.parserCommon import writableFile
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
 
 old_settings = np.seterr(all='ignore')
 

deeptools/plotCoverage.py

@@ -14,14 +14,10 @@
 import matplotlib.pyplot as plt
 import plotly.offline as py
 import plotly.graph_objs as go
-
+from importlib.metadata import version
 import deeptools.countReadsPerBin as countR
 from deeptools import parserCommon
 from deeptools.utilities import smartLabels
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
 
 old_settings = np.seterr(all='ignore')
 

deeptools/plotPCA.py

@@ -8,13 +8,9 @@
 matplotlib.rcParams['pdf.fonttype'] = 42
 matplotlib.rcParams['svg.fonttype'] = 'none'
 from deeptools import cm  # noqa: F401
-
+from importlib.metadata import version
 from deeptools.correlation import Correlation
 from deeptools.parserCommon import writableFile
-try:  # keep python 3.7 support.
-    from importlib.metadata import version
-except ModuleNotFoundError:
-    from importlib_metadata import version
 
 
 def parse_arguments(args=None):

docs/content/installation.rst

@@ -2,76 +2,61 @@ Installation
 =============
 
 Remember -- deepTools are available for **command line usage** as well as for
-**integration into Galaxy servers**!
+**integration into Galaxy servers** !
 
 .. contents:: 
     :local:
 
 Command line installation using ``conda``
 -----------------------------------------
 
-DeepTools (including the requirements) can be installed with conda:
+The recommended way to install deepTools (including its requirements) is via `miniconda <https://docs.conda.io/projects/miniconda/en/latest/>`_ or `anaconda <https://www.anaconda.com/>`_.
 
 .. code:: bash
 
     $ conda install -c bioconda deeptools
 
-Command line installation using ``pip`` from pypi
---------------------------------------------------
+Command line installation using ``pip``
+---------------------------------------
 
-Install deepTools using the following command:
-::
+deepTools can also be installed using `pip <https://pip.pypa.io/en/stable/>`_.
+You can either install the latest release from `pypi <https://pypi.org/>`_:
 
-	$ pip install deeptools
+.. code:: bash
 
-All python requirements should be automatically installed.
+	$ pip install deeptools
 
-If you need to specify a specific path for the installation of the tools, make use of `pip install`'s numerous options:
+or a specific version with:
 
 .. code:: bash
 
-    $ pip install --install-option="--prefix=/MyPath/Tools/deepTools2.0" git+https://github.com/deeptools/deepTools.git
-
+	$ pip install deeptools==3.5.3
 
-Command line installation using ``pip`` from source
----------------------------------------------------
+In case you would like to install an unreleased or development version, deepTools can also be installed from the repository:
 
-You are highly recommended to use the 'pypi installation' rather than these more complicated steps.
-
-1. Download source code
-::
+.. code:: bash
 
 	$ git clone https://github.com/deeptools/deepTools.git
-
-or if you want a particular release, choose one from https://github.com/deeptools/deepTools/releases:
-::
-
-	$ wget https://github.com/deeptools/deepTools/archive/1.5.12.tar.gz
-	$ tar -xzvf
-
-3. install the source code
-::
-
-	$ python -m build
-	$ pip install dist/*whl
+	$ cd deepTools
+	$ pip install .
 
 Galaxy installation
 --------------------
 
-deepTools can be easily integrated into a local `Galaxy <http://galaxyproject.org>`_.
+deepTools can be easily integrated into a local `Galaxy <https://galaxyproject.org>`_.
 All wrappers and dependencies are available in the `Galaxy Tool
-Shed <http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools>`_.
+Shed <https://toolshed.g2.bx.psu.edu/>`_.
 
 Installation via Galaxy API (recommended)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-First generate an `API Key <http://wiki.galaxyproject.org/Admin/API#Generate_the_Admin_Account_API_Key>`_
+First generate an `API Key <https://wiki.galaxyproject.org/Admin/API#Generate_the_Admin_Account_API_Key>`_
 for your admin user and run the the installation script:
 ::
 
 	$ python ./scripts/api/install_tool_shed_repositories.py \
 		--api YOUR_API_KEY -l http://localhost/ \
-		--url http://toolshed.g2.bx.psu.edu/ \
+		--url https://toolshed.g2.bx.psu.edu/ \
 		-o bgruening -r <revision> --name suite_deeptools \
 		--tool-deps --repository-deps --panel-section-name deepTools
 
@@ -80,7 +65,7 @@ latest revision number from the test tool shed or with the following
 command:
 ::
 
-	$ hg identify http://toolshed.g2.bx.psu.edu/repos/bgruening/suite_deeptools
+	$ hg identify https://toolshed.g2.bx.psu.edu/repos/bgruening/suite_deeptools
 
 You can watch the installation status under: Top Panel --> Admin --> Manage
 installed tool shed repositories
@@ -92,15 +77,3 @@ Installation via web browser
 -  select *Search and browse tool sheds*
 -  Galaxy tool shed --> Sequence Analysis --> deeptools
 -  install deeptools
-
-Installation with Docker
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-The deepTools Galaxy instance is also available as a docker container, for those wishing to use the Galaxy framework but who also prefer a virtualized solution. This container is quite simple to install:
-::
-
-    $ sudo docker pull quay.io/bgruening/galaxy-deeptools
-
-To start and otherwise modify this container, please see the instructions on `the docker-galaxy-stable github repository <https://github.com/bgruening/docker-galaxy-stable>`__. Note that you must use `bgruening/galaxy-deeptools` in place of `bgruening/galaxy-stable` in the examples, as the deepTools Galaxy container is built on top of the galaxy-stable container.
-
-.. tip:: For support or questions please make a post on `Biostars <http://biostars.org>`__. For feature requests or bug reports please open an issue `on github <http://github.com/deeptools/deeptools>`__.