Docstanya2 (#326)

* change API.rst and other rst files

* Changes to API

* UVCDAT_ANONYMOUS_LOG set to false

* check if git.py is there

* add gcc to environment.yml

* try docker environment.yml

* remove git.py

* chage Libregrid to regrid2

* revert

* revert

* add cdms2 class

* delet cdms2 class

* delet cdms2 class

* change conf.py os.path

* Changes to API

* Changes made to API

* Changes to API

* Changes made to API

* Changes to API

* Changes made to API

* Changes made to API

* Changes to API

* Changes to API

* Changes made to API

* Changes made to API

* Changes made to API

* push latest rst files

* Changes made to API

* Made some changes to API

* update documentations

* Changes made to API

* Changes made to API

* Changes made to API

* Changes made to Section 2 and API

* Changes made to Section 2

* Changes made to Chapter 2

* Changes made to Section 2

* Changes made to Chapters 2, 3, 4,5 and 6

* Changes made to Sections 2, 4, 7 and Appendix

* Changes made to Chapter 6 and Appendix

* Changes made to Section 2

* update summary table for API

* add generated files

* Changes made to al sections

* Changes made to Section 2 and API

* Changes made to 2 and API

* Made changes to sections 1 and 2

* Issue#231 (#232)

* fix #225 passing transiant variable as axis

* Fix macOSX

* fix ESMF and NPY_STRING

* fix data._mask comparison for numpy 1.14

* failing test from vcs added here (#234)

* failing test from vcs added here

* ok test passes again

* reverted for now

* commented out test for @durack1

* Cdmsdocsmerge (#223)

* First cdms2 documentation revamp

* latest changes

* add new files and work on avariable documentations

* fix index order

* revamp documentation

* Fixing cdms documentation (docstrings)

* update documentation

* continue to work on docs

* sphinx doctest in manual.rst

* chapter 1 continu

* add requirments.txt for read-the-doc

* move requirements.txt into docs dir

* add requirements

* Chapter 2

* add chapter 3

* finish chapter 3 started chapter 4

* flake8 python files

* chapter 4 regridding

* cdms_4 doctest

* add other chapters

* finish chapter 4

* add chapter 5

* add chapter 6

* cdms chapter 6

* fix TOC

* add chapter 7 and appendix

* merge docs

* add requirements.txt

* remove cdat_info

* remote cdat_info

* fix latex_logo png

* pin pyopenssl to 17.2.0 due to myproxyclient failure in py3

* update TOC

* work on tables and setup

* try to force jquery 3.1

* just copy js script in _static

* add highlight python

* add sample dataset page

* add sample dataset page

* work on tables for cdms_2.rst

* continue cdms2 documentations

* update cdms2 tables

* update sections

* update table

* finish chapter 2

* fix litteral error

* unlink .dodsrc for cdscan

* First changes from Tanya

* some change in chapter 1 and 2

* some changes in Chapter 2

* fix tables

* Some changes to Chapter 2

* Some Changes to Chapter 2

* Some changes made to Chapters 1, 2 and 4

* Some changes to Chapter 2

* Some Changes made to Chapter 2

* Some changes to Chapters 2, 3 and 4

* Some changes made to 1 through Appendix

* Some Changes made to Chapter 2

* Some Changes to Chapters 1, 2, 3, 6 and Appendix

* Some changes made to Chapters 1 thru 7 and appendix

* Some changes to Chpaters 1, 2 and 3

* Changes made to Chapters 1, 4, 5 and Appendix

* Some changes to Chapter 2 and 4

* Some Changes to Images, Chapter 3 and Appendix

* update logo

* add my logo

* fix chapter 1 test

* Fix python3 slice issue(setitem) and flake8 (#243)

* fix python 3 aggregation issue and flake8 (#244)

* Fix python3 slice issue(setitem) and flake8

* update to libnetcdf 4.6

* Netcdf46 (#249)

* Fix python3 slice issue(setitem) and flake8

* update to libnetcdf 4.6

* try circleci unstable label

* try version 2 circleci

* try version 2 circleci

* change workflow name

* change cdtime to cdms

* add certificate to circleci

* add fix conda-upload in circleci 2.0

* update prep_for_build version

* fix curl command

* fix cicleci for cdms

* use unstable channel change uvcdat for cdat

* build cdms on circleci 2.0

* fix circleci config.yml

* change Users/distiler to /Users/denisnadeau

* add gcc_linux

* add LDSHARED for linux

* disable cert and py results

* add gcc_linux-64

* change cdscan link

* fix myproxy

* add esmf and esmpy to py3 env

* Revert "Netcdf46 (#249)" (#250)

This reverts commit a9e29ea.

* Netcdf46 (#251)

* Fix python3 slice issue(setitem) and flake8

* update to libnetcdf 4.6

* try circleci unstable label

* try version 2 circleci

* try version 2 circleci

* change workflow name

* change cdtime to cdms

* add certificate to circleci

* add fix conda-upload in circleci 2.0

* update prep_for_build version

* fix curl command

* fix cicleci for cdms

* use unstable channel change uvcdat for cdat

* build cdms on circleci 2.0

* fix circleci config.yml

* change Users/distiler to /Users/denisnadeau

* add gcc_linux

* add LDSHARED for linux

* disable cert and py results

* add gcc_linux-64

* change cdscan link

* fix myproxy

* add esmf and esmpy to py3 env

* inverse dodsrc and curl commands

* move unlink above cdscan test

* fix ESGF test

* add new dodsrc files

* create dodsrc on-demand

* put back tests for unstable

* Netcdf46 (#252)

* Fix python3 slice issue(setitem) and flake8

* update to libnetcdf 4.6

* try circleci unstable label

* try version 2 circleci

* try version 2 circleci

* change workflow name

* change cdtime to cdms

* add certificate to circleci

* add fix conda-upload in circleci 2.0

* update prep_for_build version

* fix curl command

* fix cicleci for cdms

* use unstable channel change uvcdat for cdat

* build cdms on circleci 2.0

* fix circleci config.yml

* change Users/distiler to /Users/denisnadeau

* add gcc_linux

* add LDSHARED for linux

* disable cert and py results

* add gcc_linux-64

* change cdscan link

* fix myproxy

* add esmf and esmpy to py3 env

* inverse dodsrc and curl commands

* move unlink above cdscan test

* fix ESGF test

* add new dodsrc files

* create dodsrc on-demand

* put back tests for unstable

* instal anaconda-client before calling conda-upload

* Changes made to API

* Made some changes to API

* Changes made to API

* Changes made to API

* Changes made to API

* Changes made to Section 2 and API

* Changes made to Section 2

* Changes made to Chapter 2

* Changes made to Section 2

* Changes made to Chapters 2, 3, 4,5 and 6

* Changes made to Sections 2, 4, 7 and Appendix

* Changes made to Chapter 6 and Appendix

* Changes made to Section 2

* Changes made to al sections

* Changes made to Section 2 and API

* Changes made to 2 and API

* Made changes to sections 1 and 2

* Issue#231 (#232)

* fix #225 passing transiant variable as axis

* Fix macOSX

* fix ESMF and NPY_STRING

* fix data._mask comparison for numpy 1.14

* Fix python3 slice issue(setitem) and flake8 (#243)

* fix python 3 aggregation issue and flake8 (#244)

* Fix python3 slice issue(setitem) and flake8

* update to libnetcdf 4.6

* Netcdf46 (#249)

* Fix python3 slice issue(setitem) and flake8

* update to libnetcdf 4.6

* try circleci unstable label

* try version 2 circleci

* try version 2 circleci

* change workflow name

* change cdtime to cdms

* add certificate to circleci

* add fix conda-upload in circleci 2.0

* update prep_for_build version

* fix curl command

* fix cicleci for cdms

* use unstable channel change uvcdat for cdat

* build cdms on circleci 2.0

* fix circleci config.yml

* change Users/distiler to /Users/denisnadeau

* add gcc_linux

* add LDSHARED for linux

* disable cert and py results

* add gcc_linux-64

* change cdscan link

* fix myproxy

* add esmf and esmpy to py3 env

* Revert "Netcdf46 (#249)" (#250)

This reverts commit a9e29ea.

* Netcdf46 (#251)

* Fix python3 slice issue(setitem) and flake8

* update to libnetcdf 4.6

* try circleci unstable label

* try version 2 circleci

* try version 2 circleci

* change workflow name

* change cdtime to cdms

* add certificate to circleci

* add fix conda-upload in circleci 2.0

* update prep_for_build version

* fix curl command

* fix cicleci for cdms

* use unstable channel change uvcdat for cdat

* build cdms on circleci 2.0

* fix circleci config.yml

* change Users/distiler to /Users/denisnadeau

* add gcc_linux

* add LDSHARED for linux

* disable cert and py results

* add gcc_linux-64

* change cdscan link

* fix myproxy

* add esmf and esmpy to py3 env

* inverse dodsrc and curl commands

* move unlink above cdscan test

* fix ESGF test

* add new dodsrc files

* create dodsrc on-demand

* put back tests for unstable

* Netcdf46 (#252)

* Fix python3 slice issue(setitem) and flake8

* update to libnetcdf 4.6

* try circleci unstable label

* try version 2 circleci

* try version 2 circleci

* change workflow name

* change cdtime to cdms

* add certificate to circleci

* add fix conda-upload in circleci 2.0

* update prep_for_build version

* fix curl command

* fix cicleci for cdms

* use unstable channel change uvcdat for cdat

* build cdms on circleci 2.0

* fix circleci config.yml

* change Users/distiler to /Users/denisnadeau

* add gcc_linux

* add LDSHARED for linux

* disable cert and py results

* add gcc_linux-64

* change cdscan link

* fix myproxy

* add esmf and esmpy to py3 env

* inverse dodsrc and curl commands

* move unlink above cdscan test

* fix ESGF test

* add new dodsrc files

* create dodsrc on-demand

* put back tests for unstable

* instal anaconda-client before calling conda-upload

* Fix table titles

* Change made to Section 4

* fix bindex issue in hgrid

* Changes to all

* Corrections made to API Lib

* Changes to API

* fix ascii art

* Changes to Sections 2, 4 and 5

* Changes made to all

* Changes made to Sections 2, 6 and Appendix

* Changes made to Section 2

* Changes made to Section 2

* Changes made to Section 2 and 5

* Changes to Sections 2, 6 and 7

* Changes to API

* Changes made to API

* Made Changes to API

* Changes made to API

* Changes made to Section 4 and 7

* Changes made to API

* Changes made to API

* Revisit run tests (#262)

* migrate run_tests.py to use TestRunnerBase

* remove accidentally added tests/coverage.json

* revisit run_tests.py

* revisit run_tests.py

* revisit run_tests.py

* revisit run_tests.py

* revisit run_tests.py

* revisit run_tests.py

* revisit run_tests.py

* revisit run_tests.py

* revisit run_tests.py

* revisit run_tests.py

* revisit run_tests.py

* revisit run_tests.py

* add cacert.pem in run_tests.py when running cdms test within the lab

* add cacert.pem in run_tests.py when running cdms test within the lab

* add cacert.pem in run_tests.py when running cdms test within the lab

* add cacert.pem in run_tests.py when running cdms test within the lab - rerun tests

* add cacert.pem in run_tests.py when running cdms test within the lab - remove install from -c cdat/label/unstable

* put back -c cdat/label/unstable

* fix Axis.py

* update documentation

* fix environment dependencies

* add/remote generated files

* try to fix API.rst

* add regrid2 to docs

* Changes made to API

* fix space with parameters

* fix readthedocs using numpydoc

* update environment

* fix some autodocs

* add hgrid

* Changes made to API

* Changes made to API

* fix avariable bad location methods

* Changes to Appendix and API

* Changes to Chapter 1 and 2

* Changes made to Section 2

* Changes made to Section 2

* Changes made to Section 2

* Changes to sections 1, 2, 3 and 4

* Changes to section 2

* Changes made to entire docuemnt

* Changes to Section 1 and 2

* Changes made to Section 2

* Changes made to Sections 2 thru 6

* Changes made to Chapters 3 and 6

* add jupyter notebook

* Changes to all

* Changes to Jupyter Notebooks

* Changes to all

* update documentation for version 3.1.0

* merge documentations

* change banner and sidebar colors

* Changes to API

* fix style sheet

* Changes to API

* Changes to API

* Changes to API and Sections

* Changes to all

* will this fix master? (#292)

* Changes to Sections 1 and 2

* fix cdtime and scripts

* trigger read-the-docs

* fix more cdtime doc issues

* fix typo Default-Calendar

* fix conflicts

* pass flake8

* udpate chapter1

* Changes

* add jupyter notebook

* jupyter chapter1 fixed

* cleanup chapter 1 jupyter

* add tmp_T42_to_POP43_conserv file

* chapter 2 and chapter 3

* Changes to Jupyter Notebooks 1 and 2

* clean up

* update chapter4

* chapter 4 regridder opendap

* chapter 2 using OpenDAP

* chapter 2 using OpenDAP

* update all chapters

* Changes made to Section 2

* Changes mae to Section 1, 2 and API

* add chapter4

* Changes to Jupiter Notebooks 1 and 2

* Changes to Jupyter Notebooks 1a and 2a

* Changes to Jupyter Notebooks 1a, 2a, 3a, 4a

* Changes to Jupyter Notebooks 1a, 2a, 3a,4a, 5a

* Changes to Jupyter Notebooks 1a thru 4a

* Changes to Section 1, 2

* Changes to Sections 1 and 2

* Changes to Sections 1-3

* merge jupyter notebook

* fix flake8

* Changes to Jupyter Notebooks

* merge master

* Changes to Chapters 2, 5 and 6

* Changes to Sections 1 and 2

* Changes to API

* fix double Notes section

* Changes to API

* Changes made to API

* Change to API

* Changes to API

* Changes to API

* Changes to Sections

* Changes to Sections

* Changes to Section 1

* Changes to all

* Changes to Sections 2 and 4

* flake8 files

* Changes to sections

* update readthedocs to py3

* update environment.yml to 3.1.2

* fix environment.yml for readthedocs

* add easydev to readthedocs env yaml

* change sys.prefix to 3.7

* try to add lazy-object and change env

* enable javascript button

* Changes to Appendix B

* fix some words being cut

* Changes to Section

* Fix conflicts

* fix getWeight

* fix table alignment

* fix many documentations issues

* test table alignment

* Chapters 1 and 2

* remove chapter 5 and VCS JPG

chapter6.ipynb

@@ -339,8 +339,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.15"
+   "pygments_lexer": "ipython3",
+   "version": "3.6.8"
   }
  },
  "nbformat": 4,

docs/source/_static/agogo.css_t

@@ -21,6 +21,11 @@ table {
 tr:nth-child(even){background-color: #f2f2f2}
 tr  td:first-child { font-weight: bold }
 
+td {
+    vertical-align: top;
+    text-align: left;
+}
+
 th {    
     background-color: #01796F;
     color: #f8f8ba;

docs/source/index.rst

@@ -12,7 +12,6 @@
    manual/cdms_2
    manual/cdms_3
    manual/cdms_4
-   manual/cdms_5
    manual/cdms_6
    manual/cdms_7
    manual/cdms_appendix

docs/source/manual/cdms_1.rst

@@ -21,15 +21,12 @@ the `Python Foundation's homepage <https://python.org>`__.
 Variables
 ^^^^^^^^^
 
-The basic unit of computation in CDMS is the variable. A variable is
-essentially a multidimensional data array, augmented with a domain, a
-set of attributes, and optionally a spatial and/or temporal coordinate
-system (see `Coordinate Axes <#coordinate-axes>`__). As a data array, a variable can
-be sliced to obtain a portion of the data, and can be used in arithmetic
-computations. For example, if ``u`` and ``v`` are variables representing
-the eastward and northward components of wind speed, respectively, and
-both variables are functions of time, latitude, and longitude, then the
-velocity for time 0 (first index) can be calculated as:
+The basic unit of computation in CDMS is the variable. A variable is essentially a multidimensional data  array,
+augmented with a domain, a set of attributes, and optionally a spatial and/or temporal coordinate system
+(see `Coordinate Axes <#coordinate-axes>`__). As a data array, a variable can be sliced to obtain a portion of the 
+data, and can be used in arithmetic computations. For example, if ``u`` and ``v`` are variables representing
+the eastward and northward components of wind speed, respectively, and both variables are functions of time,
+latitude, and longitude, then the velocity for time 0 (first index) can be calculated as:
 
 ::
 
@@ -303,7 +300,7 @@ variables ``missing_value`` attribute. The data and ``missing_value``
 attribute are then written to the file.
 
 Masking is covered in `Section 2.9 <cdms_2.html#id3>`__. See also the
-documentation of the Python Numpy and MA modules, on which ``cdms.MV``
+documentation of the Python Numpy and MA modules, on which ``cdms2.MV2``
 is based, at
 
 `https://www.numpy.org/ <https://www.numpy.org/>`__.
@@ -707,7 +704,7 @@ Time Types
 ^^^^^^^^^^
 
 CDMS provides extensive support for time values in the cdtime module.
-cdtime also defines a set of calendars , specifying the number of days
+cdtime also defines a set of calendars, specifying the number of days
 in a given month.
 
 Two time types are available: relative time and component time .
@@ -731,7 +728,7 @@ units=" days since 1996-1-1". To create a relative time type:
    'days since 1996-1-1'
 
 A component time consists of the integer fields year, month, day, hour,
-minute , and the floating-point field second . For example:
+minute, and the floating-point field second. For example:
 
 ::
 
@@ -745,7 +742,7 @@ minute , and the floating-point field second . For example:
 
 The conversion functions tocomp and torel convert between the two
 representations. For instance, suppose that the time axis of a variable
-is represented in units " days since 1979" . To find the coordinate
+is represented in units " days since 1979". To find the coordinate
 value corresponding to January 1, 1990:
 
 ::