Merge pull request #27 from nlesc-nano/dev

Preparing release 1.0
nlesc-nano · Mar 22, 2021 · 6e7c433 · 6e7c433
2 parents c446a4b + ef6af37
commit 6e7c433
Show file tree

Hide file tree

Showing 14 changed files with 244 additions and 97 deletions.
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,6 +2,13 @@
 Change Log
 ##########
 
+1.0.0 [22/03/2021]
+******************
+New
+---
+* First stable versions
+
+
 0.3.0 [22/02/2021]
 ******************
 CHANGED

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -34,7 +34,7 @@ You want to make some kind of change to the code base
 
 #. (**important**) announce your plan to the rest of the community *before you start working*. This announcement should be in the form of a (new) issue;
 #. (**important**) wait until some kind of consensus is reached about your idea being a good idea;
-#. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest master commit. While working on your feature branch, make sure to stay up to date with the master branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions `here <https://help.github.com/articles/configuring-a-remote-for-a-fork/>`__ and `here <https://help.github.com/articles/syncing-a-fork/>`__);
+#. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest main commit. While working on your feature branch, make sure to stay up to date with the main branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions `here <https://help.github.com/articles/configuring-a-remote-for-a-fork/>`__ and `here <https://help.github.com/articles/syncing-a-fork/>`__);
 #. make sure the existing tests still work by running ``python setup.py test``;
 #. add your own tests (if necessary);
 #. update or expand the documentation;

diff --git a/README.rst b/README.rst
@@ -2,7 +2,7 @@
    :target: https://github.com/nlesc-nano/ceiba/actions
 .. image:: https://readthedocs.org/projects/ceiba/badge/?version=latest
    :target: https://ceiba.readthedocs.io/en/latest/?badge=latest
-.. image:: https://codecov.io/gh/nlesc-nano/ceiba/branch/master/graph/badge.svg?token=MTD70XNYEA
+.. image:: https://codecov.io/gh/nlesc-nano/ceiba/branch/main/graph/badge.svg?token=MTD70XNYEA
    :target: https://codecov.io/gh/nlesc-nano/ceiba
 .. image:: https://zenodo.org/badge/297567281.svg
    :target: https://zenodo.org/badge/latestdoi/297567281
@@ -15,15 +15,19 @@ by multidisciplinary teams across different geographical locations. Distributing
 simulations among the available resources, avoiding duplication and keeping the data safe are challenges
 that scientists face every day.
 
-Ceiba and its command line interface Ceiba-cli. Ceiba solves the problem of computing, storing and securely sharing
+Ceiba and its command line interface `Ceiba-cli <https://github.com/nlesc-nano/ceiba-cli>`_.
+Ceiba solves the problem of computing, storing and securely sharing
 computationally expensive simulation results. Researchers can save significant time and resources by easily
 computing new data and reusing existing simulation data to answer their questions.
 
-See `documentation <https://ceiba.readthedocs.io/en/latest/>`_.
+See `documentation <https://ceiba.readthedocs.io/en/latest/>`_ and `blog post <https://blog.esciencecenter.nl/building-a-web-service-to-manage-scientific-simulation-data-using-graphql-a0bbf1c3f6e9>`_.
 
 
 Installation
 ************
+The [provisioning folder](https://github.com/nlesc-nano/ceiba/tree/main/provisioning) contains the instructions
+to deploy the web service using docker. Alternatively, you can deploy the web service locally using
+the following instructions:
 
 #. 🐳 Install `Docker <https://www.docker.com/>`_
 

diff --git a/ceiba/__version__.py b/ceiba/__version__.py
@@ -1 +1 @@
-__version__ = "0.3.0"
+__version__ = "1.0.0"
diff --git a/ceiba/sdl/Query.graphql b/ceiba/sdl/Query.graphql
@@ -24,7 +24,7 @@ type Job {
   """
   _id: Int
   """
-  compute Properties
+  computed Properties
   """
   property: Property!
   """
@@ -63,7 +63,7 @@ type Property {
   """
   collection_name: String!
   """
-  Metadata associated to the given property.
+  Metadata associated with the given property.
   """
   metadata: String!
   """

diff --git a/docs/conf.py b/docs/conf.py
@@ -43,8 +43,8 @@
 # source_suffix = ['.rst', '.md']
 source_suffix = '.rst'
 
-# The master toctree document.
-master_doc = 'index'
+# The main toctree document.
+main_doc = 'index'
 
 # General information about the project.
 project = u'ceiba'
@@ -142,7 +142,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'ceiba.tex', u'ceiba Documentation',
+    (main_doc, 'ceiba.tex', u'ceiba Documentation',
      u"Felipe Zapata", 'manual'),
 ]
 
@@ -152,7 +152,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'ceiba', u'ceiba Documentation',
+    (main_doc, 'ceiba', u'ceiba Documentation',
      [author], 1)
 ]
 
@@ -163,7 +163,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'ceiba', u'ceiba Documentation',
+    (main_doc, 'ceiba', u'ceiba Documentation',
      author, 'ceiba', "Server to handle the molecular properties",
      'Miscellaneous'),
 ]
diff --git a/docs/datalayout.rst b/docs/datalayout.rst
@@ -12,23 +12,21 @@ The following schema defines how the properties are stored:
 
   # Unique identifier
   _id: Integer
+
   # Name to which the property belongs. e.g. Theory level
   collection_name: String
 
-  #Smile representing the molecule
-  smile: String
-
-  # Optimize geometry
-  geometry: Optional[String]
-
+  # Metadata associated with the given property
+  metadata: String
+  
   # Properties values as JSON
   data: Optional[String]
 
   # Input with which the property was computed encoded as JSON
   input: Optional[String]
 
 Notice that the previous schema mirros the
-`GraphQL definition of Property in the server <https://github.com/nlesc-nano/ceiba/blob/master/ceiba/sdl/Query.graphql>`_.
+`GraphQL definition of Property in the server <https://github.com/nlesc-nano/ceiba/blob/main/ceiba/sdl/Query.graphql>`_.
 
 
 Jobs collections
@@ -55,14 +53,14 @@ The following schema defines how jobs are defined:
   schedule_time: Optional[Float]
 
   # Timestamp = datatime.timestamp()
-  completion_time: Optional[Float]
+  report_time: Optional[Float]
 
   # platform where the job was run: platform.platform()
   platform: Optional[String]
    
 
 Notice that the previous schema mirros the
-`GraphQL definition of Job in the server <https://github.com/nlesc-nano/ceiba/blob/master/ceiba/sdl/Query.graphql>`_.
+`GraphQL definition of Job in the server <https://github.com/nlesc-nano/ceiba/blob/main/ceiba/sdl/Query.graphql>`_.
 
 
 .. Note::

diff --git a/docs/index.rst b/docs/index.rst
@@ -1,4 +1,4 @@
-.. ceiba documentation master file, created by
+.. ceiba documentation main file, created by
    sphinx-quickstart on Thu Jun 21 11:07:11 2018.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.

diff --git a/docs/mutations.rst b/docs/mutations.rst
@@ -1,7 +1,7 @@
 Mutations
 #########
 Mutations are defined using the `schema definition language <https://graphql.org/learn/schema/>`_.
-You can find the mutations definition at `ceiba/sdl/Mutation.graphql <https://github.com/nlesc-nano/ceiba/blob/master/ceiba/sdl/Query.graphql>`_
+You can find the mutations definition at `ceiba/sdl/Mutation.graphql <https://github.com/nlesc-nano/ceiba/blob/main/ceiba/sdl/Query.graphql>`_
 
 Mutations involved a change in the database state, requested by the client. **All the mutations required authentication**.
 

diff --git a/docs/queries.rst b/docs/queries.rst
@@ -2,7 +2,7 @@
 Queries
 #######
 Queries are defined using the `schema definition language <https://graphql.org/learn/schema/>`_.
-You can find the mutations definition `ceiba/sdl/Query.graphql <https://github.com/nlesc-nano/ceiba/blob/master/ceiba/sdl/Query.graphql>`_
+You can find the mutations definition `ceiba/sdl/Query.graphql <https://github.com/nlesc-nano/ceiba/blob/main/ceiba/sdl/Query.graphql>`_
 
 Queries involved *read-only* interactions between the client and the database.
 

diff --git a/docs/sdl_mutations.rst b/docs/sdl_mutations.rst
@@ -1,4 +1,4 @@
 Schema Mutations
 ################
 
-See `the available queries schema definitions <https://github.com/nlesc-nano/ceiba/blob/master/ceiba/sdl/Mutation.graphql>`_.
+See `the available queries schema definitions <https://github.com/nlesc-nano/ceiba/blob/main/ceiba/sdl/Mutation.graphql>`_.
diff --git a/docs/sdl_queries.rst b/docs/sdl_queries.rst
@@ -1,4 +1,4 @@
 Schema Queries
 ##############
 
-See `the available queries schema definitions <https://github.com/nlesc-nano/ceiba/blob/master/ceiba/sdl/Query.graphql>`_.
+See `the available queries schema definitions <https://github.com/nlesc-nano/ceiba/blob/main/ceiba/sdl/Query.graphql>`_.