From bdb1a8fb67884c0e66bb19795b8aa63d45d9e553 Mon Sep 17 00:00:00 2001 From: "Karol M. Langner" Date: Mon, 28 Mar 2016 00:18:52 -0700 Subject: [PATCH] Fixed generation of attributes and coverage pages (caused by Makefile sloppiness) and bump version to 1.3.2 --- _sources/attributes_dev.txt | 2 + _sources/coverage.txt | 118 +++++++++++++++---------------- _sources/coverage_dev.txt | 28 ++++---- _sources/development.txt | 2 +- _sources/index.txt | 6 +- _sources/tutorial.txt | 10 +-- attributes.html | 10 +-- attributes_dev.html | 43 ++++++----- changelog.html | 10 +-- contents.html | 12 ++-- coverage.html | 99 ++++++-------------------- coverage_dev.html | 81 ++++++++++++--------- data.html | 105 +++++++-------------------- data_dev.html | 116 +++++++++++++++++------------- data_notes.html | 16 ++--- development.html | 12 ++-- genindex.html | 14 ++-- index.html | 14 ++-- methods.html | 10 +-- objects.inv | Bin 229 -> 229 bytes old/development_sourceforge.html | 12 ++-- search.html | 10 +-- searchindex.js | 2 +- sphinx/Makefile | 27 ++++--- sphinx/attributes_dev.rst | 2 + sphinx/conf.py | 4 +- sphinx/coverage.rst | 118 +++++++++++++++---------------- sphinx/coverage_dev.rst | 28 ++++---- sphinx/development.rst | 2 +- sphinx/index.rst | 6 +- sphinx/tutorial.rst | 10 +-- tutorial.html | 24 +++---- 32 files changed, 446 insertions(+), 507 deletions(-) diff --git a/_sources/attributes_dev.txt b/_sources/attributes_dev.txt index ef49aa43..7665e84f 100644 --- a/_sources/attributes_dev.txt +++ b/_sources/attributes_dev.txt @@ -42,6 +42,7 @@ `nocoeffs`_ natural orbital coefficients array of rank 2 `nooccnos`_ natural orbital occupation numbers array of rank 1 `optdone`_ flags whether an optimization has converged Boolean + `optstatus`_ optimization status for each set of atomic coordinates array of rank 1 `scancoords`_ geometries of each scan step angstroms array of rank 3 `scanenergies`_ energies of potential energy surface list `scannames`_ names of varaibles scanned list of strings @@ -99,6 +100,7 @@ .. _`nocoeffs`: data_notes.html#nocoeffs .. _`nooccnos`: data_notes.html#nooccnos .. _`optdone`: data_notes.html#optdone +.. _`optstatus`: data_notes.html#optstatus .. _`scancoords`: data_notes.html#scancoords .. _`scanenergies`: data_notes.html#scanenergies .. _`scannames`: data_notes.html#scannames diff --git a/_sources/coverage.txt b/_sources/coverage.txt index 65ec1922..f50562d9 100644 --- a/_sources/coverage.txt +++ b/_sources/coverage.txt @@ -1,62 +1,62 @@ -================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= -attributes ADF DALTON GAMESS GAMESSUK Gaussian Jaguar Molpro NWChem ORCA Psi QChem -================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= -`aonames`_ N/A T/D √ √ √ √ √ √ √ T/D √ -`aooverlaps`_ √ N/A √ √ √ √ √ √ √ N/P T/D -`atombasis`_ T/D √ √ √ √ √ √ √ √ √ √ -`atomcharges`_ √ T/D √ √ √ √ √ √ √ √ √ -`atomcoords`_ √ √ √ √ √ √ √ √ √ √ √ -`atommasses`_ √ T/D T/D T/D √ T/D T/D T/D T/D T/D √ -`atomnos`_ √ √ √ √ √ √ √ √ √ √ √ -`atomspins`_ T/D T/D T/D T/D T/D T/D T/D T/D √ T/D √ -`ccenergies`_ N/A √ √ T/D √ T/D √ √ T/D √ √ -`charge`_ √ √ √ √ √ √ √ √ √ √ √ -`coreelectrons`_ √ √ √ √ √ √ √ √ √ √ √ -`enthalpy`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D √ -`entropy`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D √ -`etenergies`_ √ T/D √ T/D √ √ T/D T/D √ T/D √ -`etoscs`_ √ T/D √ T/D √ √ T/D T/D √ T/D √ -`etrotats`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D -`etsecs`_ √ T/D √ T/D √ √ T/D T/D √ T/D √ -`etsyms`_ √ T/D √ T/D √ √ T/D T/D √ T/D √ -`fonames`_ √ T/D N/A N/A N/A N/A N/A N/A N/A N/A N/A -`fooverlaps`_ √ T/D N/A N/A N/A N/A N/A N/A N/A N/A N/A -`fragnames`_ √ T/D N/A N/A N/A N/A N/A N/A N/A N/A N/A -`frags`_ √ T/D N/A N/A N/A N/A N/A N/A N/A N/A N/A -`freeenergy`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D √ -`gbasis`_ T/D T/D √ √ √ √ √ √ T/D √ √ -`geotargets`_ √ T/D √ √ √ √ √ √ √ √ √ -`geovalues`_ √ T/D √ √ √ √ √ √ √ √ √ -`grads`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D √ -`hessian`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D √ -`homos`_ √ √ √ √ √ √ √ √ √ √ √ -`mocoeffs`_ √ T/D √ √ √ √ √ √ √ √ √ -`moenergies`_ √ √ √ √ √ √ √ √ √ √ √ -`moments`_ √ √ √ √ T/D T/D √ √ √ √ √ -`mosyms`_ √ √ √ √ √ √ T/D √ T/D √ √ -`mpenergies`_ N/A √ √ √ √ √ √ √ T/D √ √ -`mult`_ √ √ √ √ √ √ √ √ √ √ √ -`natom`_ √ √ √ √ √ √ √ √ √ √ √ -`nbasis`_ √ √ √ √ √ √ √ √ √ √ √ -`nmo`_ √ √ √ √ √ √ √ √ √ √ √ -`nocoeffs`_ T/D T/D √ T/D √ T/D T/D T/D T/D T/D T/D -`nooccnos`_ T/D T/D √ √ √ T/D T/D T/D T/D T/D T/D -`optdone`_ √ T/D √ √ √ √ √ √ √ √ √ -`scancoords`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`scanenergies`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`scannames`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`scanparm`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`scfenergies`_ √ √ √ √ √ √ √ √ √ √ √ -`scftargets`_ √ √ √ √ √ √ √ √ √ √ √ -`scfvalues`_ √ √ √ √ √ √ √ √ √ √ √ -`temperature`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D √ -`vibanharms`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`vibdisps`_ √ T/D √ √ √ √ √ T/D √ T/D √ -`vibfreqs`_ √ T/D √ √ √ √ √ T/D √ T/D √ -`vibirs`_ √ T/D √ √ √ √ √ T/D √ T/D √ -`vibramans`_ T/D T/D √ √ √ T/D T/D T/D √ T/D √ -`vibsyms`_ T/D T/D T/D T/D √ √ √ T/D T/D T/D T/D -================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= +================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= +attributes ADF GAMESS GAMESSUK Gaussian Jaguar Molpro NWChem ORCA Psi QChem +================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= +`aonames`_ N/A √ √ √ √ √ T/D √ T/D T/D +`aooverlaps`_ √ √ √ √ √ √ √ √ N/P T/D +`atombasis`_ T/D √ √ √ √ √ √ √ √ T/D +`atomcharges`_ √ √ √ √ √ √ √ √ √ √ +`atomcoords`_ √ √ √ √ √ √ √ √ √ √ +`atommasses`_ √ T/D T/D √ T/D T/D T/D T/D T/D √ +`atomnos`_ √ √ √ √ √ √ √ √ √ √ +`atomspins`_ T/D T/D T/D T/D T/D T/D T/D √ T/D √ +`ccenergies`_ N/A √ T/D √ T/D √ √ T/D √ √ +`charge`_ √ √ √ √ √ √ √ √ √ √ +`coreelectrons`_ √ √ √ √ √ √ √ √ √ √ +`enthalpy`_ T/D T/D T/D √ T/D T/D T/D T/D T/D √ +`entropy`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D √ +`etenergies`_ √ √ T/D √ √ T/D T/D √ T/D √ +`etoscs`_ √ √ T/D √ √ T/D T/D √ T/D √ +`etrotats`_ T/D T/D T/D √ T/D T/D T/D T/D T/D T/D +`etsecs`_ √ √ T/D √ √ T/D T/D √ T/D √ +`etsyms`_ √ √ T/D √ √ T/D T/D √ T/D √ +`fonames`_ √ N/A N/A N/A N/A N/A N/A N/A N/A N/A +`fooverlaps`_ √ N/A N/A N/A N/A N/A N/A N/A N/A N/A +`fragnames`_ √ N/A N/A N/A N/A N/A N/A N/A N/A N/A +`frags`_ √ N/A N/A N/A N/A N/A N/A N/A N/A N/A +`freeenergy`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D √ +`gbasis`_ T/D √ √ √ √ √ √ T/D √ T/D +`geotargets`_ √ √ √ √ √ √ √ √ √ √ +`geovalues`_ √ √ √ √ √ √ √ √ √ √ +`grads`_ T/D T/D T/D √ T/D T/D T/D T/D T/D √ +`hessian`_ T/D T/D T/D T/D T/D √ T/D T/D T/D √ +`homos`_ √ √ √ √ √ √ √ √ √ √ +`mocoeffs`_ √ √ √ √ √ √ √ √ √ T/D +`moenergies`_ √ √ √ √ √ √ √ √ √ √ +`moments`_ √ √ √ T/D T/D √ √ √ √ √ +`mosyms`_ √ √ √ √ √ T/D √ T/D √ √ +`mpenergies`_ N/A √ √ √ √ √ √ T/D √ √ +`mult`_ √ √ √ √ √ √ √ √ √ √ +`natom`_ √ √ √ √ √ √ √ √ √ √ +`nbasis`_ √ √ √ √ √ √ √ √ √ √ +`nmo`_ √ √ √ √ √ √ √ √ √ √ +`nocoeffs`_ T/D √ T/D √ T/D T/D T/D T/D T/D T/D +`nooccnos`_ T/D √ √ √ T/D T/D T/D T/D T/D T/D +`optdone`_ √ √ √ √ √ √ √ √ √ √ +`scancoords`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`scanenergies`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`scannames`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`scanparm`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`scfenergies`_ √ √ √ √ √ √ √ √ √ √ +`scftargets`_ √ √ √ √ √ √ √ √ √ √ +`scfvalues`_ √ √ √ √ √ √ √ √ √ √ +`temperature`_ T/D T/D T/D √ T/D T/D T/D T/D T/D √ +`vibanharms`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D +`vibdisps`_ √ √ √ √ √ √ T/D √ T/D √ +`vibfreqs`_ √ √ √ √ √ √ T/D √ T/D √ +`vibirs`_ √ √ √ √ √ √ T/D √ T/D √ +`vibramans`_ T/D √ √ √ T/D T/D T/D √ T/D √ +`vibsyms`_ T/D T/D T/D √ √ √ T/D T/D T/D T/D +================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= .. _`aonames`: data_notes.html#aonames .. _`aooverlaps`: data_notes.html#aooverlaps diff --git a/_sources/coverage_dev.txt b/_sources/coverage_dev.txt index 65ec1922..e377d530 100644 --- a/_sources/coverage_dev.txt +++ b/_sources/coverage_dev.txt @@ -6,7 +6,7 @@ attributes ADF DALTON GAMESS GAMESSUK `atombasis`_ T/D √ √ √ √ √ √ √ √ √ √ `atomcharges`_ √ T/D √ √ √ √ √ √ √ √ √ `atomcoords`_ √ √ √ √ √ √ √ √ √ √ √ -`atommasses`_ √ T/D T/D T/D √ T/D T/D T/D T/D T/D √ +`atommasses`_ √ √ √ T/D √ T/D T/D T/D T/D T/D √ `atomnos`_ √ √ √ √ √ √ √ √ √ √ √ `atomspins`_ T/D T/D T/D T/D T/D T/D T/D T/D √ T/D √ `ccenergies`_ N/A √ √ T/D √ T/D √ √ T/D √ √ @@ -14,19 +14,19 @@ attributes ADF DALTON GAMESS GAMESSUK `coreelectrons`_ √ √ √ √ √ √ √ √ √ √ √ `enthalpy`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D √ `entropy`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D √ -`etenergies`_ √ T/D √ T/D √ √ T/D T/D √ T/D √ +`etenergies`_ √ √ √ T/D √ √ T/D T/D √ T/D √ `etoscs`_ √ T/D √ T/D √ √ T/D T/D √ T/D √ `etrotats`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D -`etsecs`_ √ T/D √ T/D √ √ T/D T/D √ T/D √ -`etsyms`_ √ T/D √ T/D √ √ T/D T/D √ T/D √ +`etsecs`_ √ √ √ T/D √ √ T/D T/D √ T/D √ +`etsyms`_ √ √ √ T/D √ √ T/D T/D √ T/D √ `fonames`_ √ T/D N/A N/A N/A N/A N/A N/A N/A N/A N/A `fooverlaps`_ √ T/D N/A N/A N/A N/A N/A N/A N/A N/A N/A `fragnames`_ √ T/D N/A N/A N/A N/A N/A N/A N/A N/A N/A `frags`_ √ T/D N/A N/A N/A N/A N/A N/A N/A N/A N/A `freeenergy`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D √ -`gbasis`_ T/D T/D √ √ √ √ √ √ T/D √ √ -`geotargets`_ √ T/D √ √ √ √ √ √ √ √ √ -`geovalues`_ √ T/D √ √ √ √ √ √ √ √ √ +`gbasis`_ T/D √ √ √ √ √ √ √ √ √ √ +`geotargets`_ √ √ √ √ √ √ √ √ √ √ √ +`geovalues`_ √ √ √ √ √ √ √ √ √ √ √ `grads`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D √ `hessian`_ T/D T/D T/D T/D T/D T/D √ T/D T/D T/D √ `homos`_ √ √ √ √ √ √ √ √ √ √ √ @@ -41,7 +41,8 @@ attributes ADF DALTON GAMESS GAMESSUK `nmo`_ √ √ √ √ √ √ √ √ √ √ √ `nocoeffs`_ T/D T/D √ T/D √ T/D T/D T/D T/D T/D T/D `nooccnos`_ T/D T/D √ √ √ T/D T/D T/D T/D T/D T/D -`optdone`_ √ T/D √ √ √ √ √ √ √ √ √ +`optdone`_ √ √ √ √ √ √ √ √ √ √ √ +`optstatus`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D T/D `scancoords`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D `scanenergies`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D `scannames`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D @@ -51,11 +52,11 @@ attributes ADF DALTON GAMESS GAMESSUK `scfvalues`_ √ √ √ √ √ √ √ √ √ √ √ `temperature`_ T/D T/D T/D T/D √ T/D T/D T/D T/D T/D √ `vibanharms`_ T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D T/D -`vibdisps`_ √ T/D √ √ √ √ √ T/D √ T/D √ -`vibfreqs`_ √ T/D √ √ √ √ √ T/D √ T/D √ -`vibirs`_ √ T/D √ √ √ √ √ T/D √ T/D √ -`vibramans`_ T/D T/D √ √ √ T/D T/D T/D √ T/D √ -`vibsyms`_ T/D T/D T/D T/D √ √ √ T/D T/D T/D T/D +`vibdisps`_ √ √ √ √ √ √ √ T/D √ T/D √ +`vibfreqs`_ √ √ √ √ √ √ √ T/D √ T/D √ +`vibirs`_ √ √ √ √ √ √ √ T/D √ T/D √ +`vibramans`_ T/D √ √ √ √ T/D T/D T/D √ T/D √ +`vibsyms`_ T/D √ T/D T/D √ √ √ T/D T/D T/D T/D ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= ================= .. _`aonames`: data_notes.html#aonames @@ -99,6 +100,7 @@ attributes ADF DALTON GAMESS GAMESSUK .. _`nocoeffs`: data_notes.html#nocoeffs .. _`nooccnos`: data_notes.html#nooccnos .. _`optdone`: data_notes.html#optdone +.. _`optstatus`: data_notes.html#optstatus .. _`scancoords`: data_notes.html#scancoords .. _`scanenergies`: data_notes.html#scanenergies .. _`scannames`: data_notes.html#scannames diff --git a/_sources/development.txt b/_sources/development.txt index dc795cdd..061f474c 100644 --- a/_sources/development.txt +++ b/_sources/development.txt @@ -91,7 +91,7 @@ The input files for tests, which are logfiles from computational chemistry progr .. _`Travis CI`: https://travis-ci.org/cclib/cclib -.. |travis_prod| image:: https://travis-ci.org/cclib/cclib.svg?branch=v1.3.1 +.. |travis_prod| image:: https://travis-ci.org/cclib/cclib.svg?branch=v1.3.2 .. |travis_master| image:: https://travis-ci.org/cclib/cclib.svg?branch=master .. _`data directory`: https://github.com/cclib/cclib/tree/master/test diff --git a/_sources/index.txt b/_sources/index.txt index 5fcc2d0b..1ed11690 100644 --- a/_sources/index.txt +++ b/_sources/index.txt @@ -12,7 +12,7 @@ The goals of cclib are centered around the reuse of data obtained from these pro Summary ------- -The current version is **cclib 1.3.1** (see the changelog_ for what's new) and parses output files from the following programs (version in parentheses are tested): +The current version is **cclib 1.3.2** (see the changelog_ for what's new) and parses output files from the following programs (version in parentheses are tested): - ADF_ (versions 2007 and 2013) - Firefly_, formerly known as PC GAMESS (version 8.0) @@ -28,7 +28,7 @@ Many types of output data are parsed by cclib, including atom coordinates, orbit How to use cclib ---------------- -You can download the `source package for cclib 1.3.1`_ or the `current development version`_ (from the `github repository`_). For information on packages available in various Linux distribution, installing the source code and requirements, as well as basic usage, the tutorial_ is a good place to start. +You can download the `source package for cclib 1.3.2`_ or the `current development version`_ (from the `github repository`_). For information on packages available in various Linux distribution, installing the source code and requirements, as well as basic usage, the tutorial_ is a good place to start. If you need further help, find a bug, need new features or have any question, please send email to the `mailing list`_ or submit an issue to the `tracker`_. @@ -62,7 +62,7 @@ If you use cclib in your scientific work, please support our work by adding a re .. _Molpro: http://www.molpro.net/ .. _ORCA: http://www.thch.uni-bonn.de/tc/orca/ -.. _`source package for cclib 1.3.1`: https://github.com/cclib/cclib/releases/download/v1.3.1/cclib-1.3.1.zip +.. _`source package for cclib 1.3.2`: https://github.com/cclib/cclib/releases/download/v1.3.2/cclib-1.3.2.zip .. _`current development version`: https://github.com/cclib/cclib/archive/master.zip .. _`github repository`: https://github.com/cclib/cclib .. _`mailing list`: https://lists.sourceforge.net/lists/listinfo/cclib-users diff --git a/_sources/tutorial.txt b/_sources/tutorial.txt index 4d36849b..cac66443 100644 --- a/_sources/tutorial.txt +++ b/_sources/tutorial.txt @@ -66,9 +66,9 @@ There are in fact two packages, `python-cclib`_ containing the Python module, an Manual download and install --------------------------- -The source code of the newest release of cclib (version 1.3.1) is distributed as: - * A .zip file: https://github.com/cclib/cclib/releases/download/v1.3.1/cclib-1.3.1.zip - * A .tar.gz file: https://github.com/cclib/cclib/releases/download/v1.3.1/cclib-1.3.1.tar.gz +The source code of the newest release of cclib (version 1.3.2) is distributed as: + * A .zip file: https://github.com/cclib/cclib/releases/download/v1.3.2/cclib-1.3.2.zip + * A .tar.gz file: https://github.com/cclib/cclib/releases/download/v1.3.2/cclib-1.3.2.tar.gz * Windows binary installers (see the `newest release page`_) On Windows, if you choose to download the .exe files instead, you can install simply by doubleclicking on the file. To uninstall, use the "Add and Remove Programs" menu in the Control Panel. @@ -95,7 +95,7 @@ To test, trying importing '''cclib''' at the Python prompt. You should see somet '1.1' >>> -.. _`newest release page`: https://github.com/cclib/cclib/releases/tag/v1.3.1 +.. _`newest release page`: https://github.com/cclib/cclib/releases/tag/v1.3.2 What next? ---------- @@ -107,4 +107,4 @@ What next? * Write some computational chemistry algorithms using information parsed from cclib and donate the code to the project .. _`parsed data`: data.html -.. _`data notes`: data_notes.html \ No newline at end of file +.. _`data notes`: data_notes.html diff --git a/attributes.html b/attributes.html index cb090b7e..3607fc8d 100644 --- a/attributes.html +++ b/attributes.html @@ -8,7 +8,7 @@ - <no title> — cclib 1.3.1 documentation + <no title> — cclib 1.3.2 documentation @@ -30,7 +30,7 @@ - + @@ -83,7 +83,7 @@
  • What next?
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  • Parsed data (version 1.3.1)
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  • Parsed data (version 1.3.1)
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  • Parsed data (version 1.3.1)