Commit 8d44d758 authored by Fabrice Allain's avatar Fabrice Allain
Browse files

Updated doc

parent 91485ecf
......@@ -6,6 +6,8 @@ RUN yum install -y python2-pip python-devel gcc make git
RUN pip install --upgrade pip ; pip install --upgrade setuptools; pip install sphinx; pip install numpy; pip install matplotlib; pip install coverage; pip install pytest; pip install pytest-cov
RUN wget http://www2.ccpn.ac.uk/download/ccpnmr/analysis2.4.2.tar.gz; tar xvzf analysis2.4.2.tar.gz; export CCPNMR_TOP_DIR=$(pwd)/ccpnmr; export PYTHONPATH=${PYTHONPATH}:$CCPNMR_TOP_DIR/ccpnmr2.4/python
RUN mkdir build-aria
ADD aria /build-aria/aria
ADD *.py PKG-INFO /build-aria/
......
......@@ -17,7 +17,7 @@ de Novo Ambiguous Restraints for Iterative Assignment
:alt: DOI status
``ariaec`` is a Python_ library that provides *de novo* structure prediction
**ariaec** is a Python_ library that provides *de novo* structure prediction
based on ARIA_ pipeline and evolutionary restraints inferred from co-evolution.
......@@ -33,20 +33,19 @@ Quick Start
Be sure to check if the following packages are correctly installed with
your python installation or virtual environment.
* ``pip`` (>= 9.0)
* ``setuptools`` (>= 18.0)
* ``numpy`` (>= 1.11)
* **pip** (>= 9.0)
* **setuptools** (>= 18.0)
* **numpy** (>= 1.11)
Then the easiest solution is to call the ``pip`` command below :
Then the easiest solution is to call the **pip** command below :
``pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec``
.. TODO change line to code block console when gitlab rst rendering will
be solved
.. code-block:: console
$ pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec
Another possibility is to download the ZIP_ or TAR_ version from Gitlab_,
extract the files and run ``pip install .`` inside the new directory
Even though it is not recommanded, another possibility is to download the ZIP_
or TAR_ version from Gitlab_, extract the files and run ``pip install .``
inside the new directory.
For more information about installation and usage, please refer to the
`ARIAEC documentation <http://bis-aria.pages.pasteur.fr/ariaec>`_.
......
......@@ -13,7 +13,6 @@ Copyright (C) Benjamin Bardiaux, Michael Habeck, Therese Malliavin,
All rights reserved.
NO WARRANTY. This software package is provided 'as is' without warranty of
any kind, expressed or implied, including, but not limited to the implied
warranties of merchantability and fitness for a particular purpose or
......
This diff is collapsed.
......@@ -32,7 +32,7 @@ import os
import re
import string
import core.legacy.DeleteCnsComments as DeleteCnsComments
import aria.core.legacy.DeleteCnsComments as DeleteCnsComments
__author__ = "$Author: bardiaux $"
__revision__ = "$Revision: 1.1.1.1 $"
......
:autogenerated:
aria.aria2 module
=================
.. currentmodule:: aria.aria2
.. automodule:: aria.aria2
:members: check_numeric_slice, check_python, convert, convert_data, default_printer, get_path, get_project_name, invalid_args, load_project, main, parse_args, print_sequence, print_spectrum, print_template_structure, project_info, run_aria, run_gui, setup_aria, show_help, welcome, write_project_template
:undoc-members:
:show-inheritance:
:member-order: bysource
Summary
-------
Functions:
.. autosummary::
:nosignatures:
check_numeric_slice
check_python
convert
convert_data
default_printer
get_path
get_project_name
invalid_args
load_project
main
parse_args
print_sequence
print_spectrum
print_template_structure
project_info
run_aria
run_gui
setup_aria
show_help
welcome
write_project_template
Reference
---------
\ No newline at end of file
:autogenerated:
aria.check module
=================
.. currentmodule:: aria.check
.. automodule:: aria.check
:members: check_ccpn, check_numeric, check_numeric_slice, check_pylab, check_python, check_scientific, check_tix
:undoc-members:
:show-inheritance:
:member-order: bysource
Summary
-------
Functions:
.. autosummary::
:nosignatures:
check_ccpn
check_numeric
check_numeric_slice
check_pylab
check_python
check_scientific
check_tix
Reference
---------
\ No newline at end of file
:autogenerated:
aria.core.ccpn2top module
=========================
.. currentmodule:: aria.core.ccpn2top
.. automodule:: aria.core.ccpn2top
:members:
:members: createAriaAtom, createAriaResidue, createAriaTopology, setupEquivalentGroup
:undoc-members:
:show-inheritance:
:member-order: bysource
Summary
-------
Functions:
.. autosummary::
:nosignatures:
createAriaAtom
createAriaResidue
createAriaTopology
setupEquivalentGroup
Reference
---------
\ No newline at end of file
:autogenerated:
aria.core.ccpn_conversion module
================================
.. currentmodule:: aria.core.ccpn_conversion
.. automodule:: aria.core.ccpn_conversion
:members:
:members: CCPNConverter, find_ccpn_atom, map_aria_atoms, map_dimensions
:undoc-members:
:show-inheritance:
:member-order: bysource
Summary
-------
Classes:
.. autosummary::
:nosignatures:
CCPNConverter
Functions:
.. autosummary::
:nosignatures:
find_ccpn_atom
map_aria_atoms
map_dimensions
Reference
---------
\ No newline at end of file
:autogenerated:
aria.core.exportToCcpn module
=============================
.. currentmodule:: aria.core.exportToCcpn
.. automodule:: aria.core.exportToCcpn
:members:
:members: copyFixedResonance, getAria2AtomSetPairs, getAria2ObjectsFromPickle, getAria2SpinSystems, getAriaRun, getBoundResonance, getCcpnSeqfromAriaChain, getChainFromAria2, getChainFromAria2Atom, getChainsFromAria2, getConstraintFromAria2, getConstraintsFromAria2, getFixedAtomSet, getFixedResonanceFromAria2Atom, getPeakAssignmentsFromAria2, getResonanceFromAria2Atom, getStructuresFromAria2Dir, getStructuresFromAria2Dir_Analysis, getStructuresFromAria2Dir_Format, getViolationFromAria2, importAria2RunData
:undoc-members:
:show-inheritance:
:member-order: bysource
Summary
-------
Functions:
.. autosummary::
:nosignatures:
copyFixedResonance
getAria2AtomSetPairs
getAria2ObjectsFromPickle
getAria2SpinSystems
getAriaRun
getBoundResonance
getCcpnSeqfromAriaChain
getChainFromAria2
getChainFromAria2Atom
getChainsFromAria2
getConstraintFromAria2
getConstraintsFromAria2
getFixedAtomSet
getFixedResonanceFromAria2Atom
getPeakAssignmentsFromAria2
getResonanceFromAria2Atom
getStructuresFromAria2Dir
getStructuresFromAria2Dir_Analysis
getStructuresFromAria2Dir_Format
getViolationFromAria2
importAria2RunData
Reference
---------
\ No newline at end of file
:autogenerated:
aria.core.gui.ccpnGui module
============================
.. currentmodule:: aria.core.gui.ccpnGui
.. automodule:: aria.core.gui.ccpnGui
:members:
:members: gui_select_constraintList, gui_select_constraintStore, gui_select_ensemble, gui_select_model, gui_select_molSystem, gui_select_peakList, gui_select_shiftList, gui_select_structureGeneration, selectConstraintList, setupDialog, setupDialogAndSelect
:undoc-members:
:show-inheritance:
:member-order: bysource
Summary
-------
Functions:
.. autosummary::
:nosignatures:
gui_select_constraintList
gui_select_constraintStore
gui_select_ensemble
gui_select_model
gui_select_molSystem
gui_select_peakList
gui_select_shiftList
gui_select_structureGeneration
selectConstraintList
setupDialog
setupDialogAndSelect
Reference
---------
\ No newline at end of file
:autogenerated:
aria.core.importFromCcpn module
===============================
.. currentmodule:: aria.core.importFromCcpn
.. automodule:: aria.core.importFromCcpn
:members:
:members: addSecStrucToAriaRes, checkExpTransfers, dumpModel, dumpRestraintsList, findCcpnDataDim, getAcqRefExpDimRef, getAriaAtomsFromResonance, getAriaDistanceRestraintsList, getCcpnChain, getCcpnChains, getCcpnConstraintList, getCcpnConstraintLists, getCcpnExperimentData, getCcpnExperimentShiftList, getCcpnModel, getCcpnModels, getCcpnPeakAndShiftLists, getCcpnPeakList, getCcpnShiftList, getKeysFromString, getModels, getNoesyPeakLists, getObjectKeyString, getObjectKeys, getObjectsKeyString, getShiftLists, getStructureEnsembles, makeAriaAtom, makeAriaChain, makeAriaChemicalShift, makeAriaMolecule, makeAriaResidue, makeAriaShiftList, makeAriaSpectrum
:undoc-members:
:show-inheritance:
:member-order: bysource
Summary
-------
Functions:
.. autosummary::
:nosignatures:
addSecStrucToAriaRes
checkExpTransfers
dumpModel
dumpRestraintsList
findCcpnDataDim
getAcqRefExpDimRef
getAriaAtomsFromResonance
getAriaDistanceRestraintsList
getCcpnChain
getCcpnChains
getCcpnConstraintList
getCcpnConstraintLists
getCcpnExperimentData
getCcpnExperimentShiftList
getCcpnModel
getCcpnModels
getCcpnPeakAndShiftLists
getCcpnPeakList
getCcpnShiftList
getKeysFromString
getModels
getNoesyPeakLists
getObjectKeyString
getObjectKeys
getObjectsKeyString
getShiftLists
getStructureEnsembles
makeAriaAtom
makeAriaChain
makeAriaChemicalShift
makeAriaMolecule
makeAriaResidue
makeAriaShiftList
makeAriaSpectrum
Reference
---------
\ No newline at end of file
:autogenerated:
aria.core.legacy.PpmList module
===============================
.. currentmodule:: aria.core.legacy.PpmList
.. automodule:: aria.core.legacy.PpmList
:members:
:members: Atom, PpmList
:undoc-members:
:show-inheritance:
:member-order: bysource
Summary
-------
Classes:
.. autosummary::
:nosignatures:
Atom
PpmList
Reference
---------
\ No newline at end of file
:autogenerated:
aria.core.legacy.test package
=============================
.. automodule:: aria.core.legacy.test
Submodules:
.. toctree::
:maxdepth: 1
aria.core.legacy.test.test_AminoAcid
aria.core.legacy.test.test_Comparisons
aria.core.legacy.test.test_AminoAcid module
===========================================
.. automodule:: aria.core.legacy.test.test_AminoAcid
:members:
:undoc-members:
:show-inheritance:
:autogenerated:
aria.core.legacy.test.test_Comparisons module
=============================================
.. currentmodule:: aria.core.legacy.test.test_Comparisons
.. automodule:: aria.core.legacy.test.test_Comparisons
:autogenerated:
aria.core.test package
======================
.. automodule:: aria.core.test
......@@ -10,13 +10,6 @@ aria package
:show-inheritance:
Submodules:
.. toctree::
:maxdepth: 1
aria.aria2
aria.check
Subpackages:
.. toctree::
......
......@@ -89,7 +89,8 @@ def run_apidoc(_):
import better_apidoc
better_apidoc.main(
['better-apidoc', '-t', './_templates', '--force', '--no-toc',
'--separate', '-o', './api', '../aria', '../*test*'])
'--separate', '-o', './api', '../aria', '../*test*',
'../aria/aria2.py', '../aria/check.py'])
def setup(app):
......@@ -205,6 +206,12 @@ html_context = {
'css_files': [
'_static/theme_overrides.css', # override wide tables in RTD theme
],
"display_gitlab": True, # Integrate Gitlab
"gitlab_host": "gitlab.pasteur.fr",
"gitlab_user": "bis-aria", # Username
"gitlab_repo": "ariaec", # Repo name
"gitlab_version": "master", # Version
"conf_py_path": "/docs/", # Path in the checkout to the docs root
}
html_favicon = "_static/favicon.ico"
......
......@@ -3,6 +3,7 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
:gitlab_url:
.. include:: ../README.rst
......
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