Release 1.3

CONTRIBUTING.md

@@ -1,15 +1,15 @@
 # Contributing to senaite.core
 
-Third-party contributions are essential for keeping `senaite.core` continuously 
-improving. We simply cannot access the huge number of platforms and myriad 
-configurations for running `senaite.core`. We want to keep it as easy as 
-possible to contribute changes that get things working in your environment. 
-There are a few guidelines that we need contributors to follow so that we can 
+Third-party contributions are essential for keeping `senaite.core` continuously
+improving. We simply cannot access the huge number of platforms and myriad
+configurations for running `senaite.core`. We want to keep it as easy as
+possible to contribute changes that get things working in your environment.
+There are a few guidelines that we need contributors to follow so that we can
 have a chance of keeping on top of things.
 
-The following is a set of guidelines for contributing to senaite.core, which is 
-hosted in the [SENAITE Organization](https://github.com/senaite) on GitHub. 
-These are just guidelines, not rules. Use your best judgment, and feel free to 
+The following is a set of guidelines for contributing to senaite.core, which is
+hosted in the [SENAITE Organization](https://github.com/senaite) on GitHub.
+These are just guidelines, not rules. Use your best judgment, and feel free to
 propose changes to this document in a [pull request](#how-to-submit-a-pull-request).
 
 ## Code of Conduct
@@ -63,21 +63,21 @@ contribute to the source code.
    https://github.com/senaite/senaite.core/fork). This will copy the whole
    `senaite.core` repository to your personal account.
 
-   3. Then, go to your favourite working folder in your computer and clone your 
+   3. Then, go to your favourite working folder in your computer and clone your
    forked repository by typing (replacing ```YOUR_USERNAME``` by
    the actual username of your GitHub account):
 
           $ git clone https://github.com/YOUR_USERNAME/senaite.core
 
-   4. Your forked repository https://github.com/YOUR_USERNAME/senaite.core will 
-   receive the default name of `origin`. You can also add the original 
+   4. Your forked repository https://github.com/YOUR_USERNAME/senaite.core will
+   receive the default name of `origin`. You can also add the original
    `senaite.core` repository, which is usually called `upstream`:
 
           $ cd senaite.core
           $ git remote add upstream https://github.com/senaite/senaite.core.git
 
-To verify the new upstream repository you have specified for your fork, type 
-`git remote -v`. You should see the URL for your fork as `origin`, and the URL 
+To verify the new upstream repository you have specified for your fork, type
+`git remote -v`. You should see the URL for your fork as `origin`, and the URL
 for the original repository as `upstream`:
 
 ```
@@ -99,15 +99,15 @@ $ git pull upstream master
 ```
 
 Now you can do changes, add files, do commits (please take a look at
-[how to write good commit messages](https://chris.beams.io/posts/git-commit/)!) 
+[how to write good commit messages](https://chris.beams.io/posts/git-commit/)!)
 and push them to your repository:
 
 ```
 $ git push origin my_feature
 ```
 
 If there have been new pushes to the `master` branch of the `upstream`
-repository since the last time you pulled from it, you might want to put your 
+repository since the last time you pulled from it, you might want to put your
 commits on top of them (this is mandatory for pull requests):
 
 ```
@@ -129,7 +129,7 @@ pros and cons between doing a `gir rebase` or `git merge`. Good documentation on
 this regard can be found in the [Atlassian's Merging vs. Rebasing tutorial](
 https://www.atlassian.com/git/tutorials/merging-vs-rebasing).
 
-Note this `git rebase` or `git merge` is required for keeping your branch 
+Note this `git rebase` or `git merge` is required for keeping your branch
 aligned with the latest code from the repos. The incorporation of your work into
 `master` through a Pull Request will always be done using `git merge`.
 
@@ -141,15 +141,15 @@ GitHub repository, switch to your `my_feature` branch, and click the
 _**Pull Request**_ button, which will do all the work for you. Ensure the
 comparison is done with the `master` branch unless you forked from another one.
 
-Once a pull request is sent, the Developer Team will review the set of changes, 
+Once a pull request is sent, the Developer Team will review the set of changes,
 discuss potential modifications, and even push follow-up commits if necessary.
 
 Some things that will increase the chance that your pull request is accepted:
 
  * Write tests.
  * Follow [Plone's Python styleguide](https://docs.plone.org/develop/styleguide/python.html).
  * Write a descriptive and detailed summary. Please consider that reviewing pull
-   requests is hard, so include as much information as possible to make your 
+   requests is hard, so include as much information as possible to make your
    pull request's intent clear.
  * Do not address multiple bugfixes or features in the same Pull Request.
  * Include whitespace and formatting changes in discrete commits.
@@ -161,17 +161,17 @@ For more details about Git usage, please check out Chapters 1 and 2 from
 
 ## Contributing with new ideas
 
-All suggestions and proposals are welcome. We strongly believe that the 
-feedback of the community is an important asset to make a better project. With 
-the aim to get the most of these contributions, but without interfering with 
-the undergoing work regarding to issues and Pull Requests, we've created a 
+All suggestions and proposals are welcome. We strongly believe that the
+feedback of the community is an important asset to make a better project. With
+the aim to get the most of these contributions, but without interfering with
+the undergoing work regarding to issues and Pull Requests, we've created a
 [Community discussion board](
-https://community.senaite.org). This is the right place if 
+https://community.senaite.org). This is the right place if
 you are willing to discuss about new ideas, further steps or improvements.
 
-If you want to keep in touch with the community members and up-to-date 
+If you want to keep in touch with the community members and up-to-date
 with the latest discussions, please join to the [Gitter community channel](
 https://gitter.im/senaite/Lobby).
 
-If you want to stay informed about senaite at easy pace, don't forget 
+If you want to stay informed about senaite at easy pace, don't forget
 to subscribe to our [users list](https://sourceforge.net/projects/senaite/lists/senaite-users)

CONTRIBUTORS.rst

@@ -7,33 +7,37 @@ Contributions to master, excluding merge commits, sorted by number of
 contributions descending.
 
 - Campbell McKellar-Basset, rockfruit@users.noreply.github.com
-- Jordi Puiggené, jpuiggene@naralabs.com
+- Jordi Puiggené, jp@naralabs.com
 - Pau Soliva, psoliva@naralabs.com
 - Ramon Bartl, rb@ridingbytes.com
 - Nihad Mammadli, 1992.nihad@gmail.com
 - Anneline Sweetname, anneline@bikalabs.com
-- Juan Gallostra, jgallostra@naralabs.com
+- Juan Gallostra, juangallostra@users.noreply.github.com
 - Godfrey Leibbrandt, godfrey@bikalabs.com
 - Mike Metcalfe, mike@metcalfe.co.za
 - Jurie-Jan Botha, juriejanbotha@gmail.com
-- Inus Scheepers, inus@bikalabs.com
 - Lunga Baliwe, lunga001@gmail.com
+- Inus Scheepers, inus@bikalabs.com
 - Oliver Roch, oliver.roch@d9t.de
 - Alexander Karlsson, ak.zylinx@gmail.com
 - Anton Feun, anton@satides.co.za
 - Jayadeep Karnati, karnatijayadeep@gmail.com
 - Lemoene, lemoene@bikalabs.com
 - Dhruv Khattar, dhruv@khattarindia.com
 - witekdev, witekdev@gmail.com
+- Anderson Smith, andersonsmith183@gmail.com
 - Javis Sullivan, javissullivan@gmail.com
 - Pieter van der Merwe, pieter_vdm@debortoli.com.au
-- Anderson Smith, andersonsmith183@gmail.com
 - Jean Jordaan, jean.jordaan@gmail.com
+- MoffatMore, 12894381+MoffatMore@users.noreply.github.com
+- krishan Chopra, krishanchopra61@yahoo.in
+- jpsinghgoud, jaipal.singh@research.iiit.ac.in
+- Stefan Gruber, s.gruber@liscon.de
 - Aleksandr Melnikov, aleksandr.melnikov@limelyte.com
 - Henrique Chehad, hchehad@gmail.com
-- jpsinghgoud, jaipal.singh@research.iiit.ac.in
 - goelakash, goelakash93@gmail.com
 - Manav Batra, manavbatra@outlook.com
+- mimishons, shoniwam@nmrl.org.zw
 
 
 Translators
@@ -134,5 +138,7 @@ Translators
 - yuan314159, yuan314159@gmail.com, Chinese (China) (zh_CN)
 - Cheng Jin, 17067405@qq.com, Chinese (China) (zh_CN)
 - Inus Scheepers, inus@animatica.co.za, Chinese (China) (zh_CN)
+- prosper wang, prosperwang@163.com, Chinese (China) (zh_CN)
 - Rui Tang, bio.nanoparticle@gmail.com, Chinese (Taiwan) (zh_TW)
 - Matthew Tsui, mtsui@app2one.com, Chinese (Taiwan) (zh_TW)
+- Liz Sung, lesliesong@gmail.com, Chinese (Taiwan) (zh_TW)

README.rst

@@ -1,16 +1,10 @@
-.. raw:: html
+.. image:: https://raw.githubusercontent.com/senaite/senaite.core/master/static/logo_pypi.png
+   :target: https://github.com/senaite/senaite.core
+   :alt: senaite.core
+   :height: 128px
 
-  <div align="center">
-    <h1>
-      <a href="https://github.com/senaite/senaite.core">
-        <div>
-          <img src="https://raw.githubusercontent.com/senaite/senaite.core/master/static/senaite-logo.png" alt="senaite.core" height="64" />
-        </div>
-      </a>
-    </h1>
-  </div>
-
-— **SENAITE.CORE**: *Open Source LIMS Core based on the CMS Plone*
+*Open Source LIMS Core based on the CMS Plone*
+==============================================
 
 .. image:: https://img.shields.io/pypi/v/senaite.core.svg?style=flat-square
     :target: https://pypi.python.org/pypi/senaite.core
@@ -30,6 +24,12 @@
 .. image:: https://img.shields.io/github/contributors/senaite/senaite.core.svg?style=flat-square
     :target: https://github.com/senaite/senaite.core/blob/master/CONTRIBUTORS.rst
 
+.. image:: https://img.shields.io/badge/Built%20with-%E2%9D%A4-red.svg
+   :target: https://github.com/senaite/senaite.core
+
+.. image:: https://img.shields.io/badge/Made%20for%20SENAITE-%E2%AC%A1-lightgrey.svg
+   :target: https://www.senaite.com
+
 
 Introduction
 ============
@@ -79,7 +79,7 @@ Feedback and support
 License
 =======
 
-**SENAITE.CORE** Copyright (C) 2018 Senaite Foundation
+**SENAITE.CORE** Copyright (C) 2018-2019 Senaite Foundation
 
 This software, henceforth "SENAITE.CORE" is an add-on for the
 `Plone CMS <https://plone.org/>`_ and a derivative work of BIKA LIMS.

RELEASE_NOTES.rst

@@ -6,19 +6,40 @@ Update from 1.2.9 to 1.3.0
 
 **IMPORTANT: Plan the upgrade with enough time**
 
-Version 1.3.0 is not a hotfixes release, so this update comes with a lot of
-changes that require additional care when planning the update. If you have your
-own add-on, please review the changes to see beforehand if some parts of your
-add-on need to be modified.
-
-Amongst these changes, the refactoring of Workflows logic will have a huge
-impact on how long this update will require for its completion.
-
-To reduce the time for the upgrade to complete, we suggest the following tips:
-
-  - Do a backup of both your code and the database before proceed.
-
-  - Try to have as much analyses in verified state as possible.
+Version 1.3.0 is not a hotfix release, it rather comes with a lot of changes
+that require additional care when planning the update. If you have your own
+add-on, please review the changes to check beforehand if some parts of your
+add-on require modifications.
+
+This update will take long (up to 5h for instances with large amounts of data).
+Therefore, is recommended to plan and allocate enough resources for the process
+to complete beforehand. For big databases, RAM is a critical factor to be
+considered before upgrading. Worth to mention that the following tips are
+strongly recommended before proceeding with the upgrade:
+
+- Do a zeopack
+- Do a backup of both your code and database
+- Try to have as much analyses in verified/published statuses as possible
+- Stop unnecessary applications and services that may consume RAM
+- Start with a clean log file
+
+Most of the base code has been refactored keeping in mind the following
+objectives:
+
+- Less complexity: less code, better code
+- High test coverage: lower chance of undetected bugs
+- Boost performance: better experience, with no delays
+- Improve security: rely on Zope's security policies
+- Code responsibility: focus on core functionalities and let other add-ons to
+  deal with the rest (`senaite.lims`, `senaite.core.listing`, etc.)
+
+Besides of this refactoring, this version also comes with a myriad of new
+functionalities and enhancements: full-fledged sample partitions, reinvented
+listings and results entry, new adapters for extensibility, etc.
+
+Version 1.3 is the result of hard, but exciting work at same time. Four months
+of walking through valleys of tears and fighting hydras. Four exciting months to
+be proud of.
 
 
 Update from 1.2.8 to 1.2.9
@@ -28,17 +49,17 @@ Update from 1.2.8 to 1.2.9
 This update might take long depending on the number of Analyses, Analysis
 Requests and Samples registered in the system:
 
-  - Role mappings updated for Analaysis Requests and Samples (rejection)
-    https://github.com/senaite/senaite.core/pull/1041
+- Role mappings updated for Analaysis Requests and Samples (rejection)
+  https://github.com/senaite/senaite.core/pull/1041
 
-  - Recatalog of invalidated/retest Analysis Requests (invalidation)
-    https://github.com/senaite/senaite.core/pull/1027
+- Recatalog of invalidated/retest Analysis Requests (invalidation)
+  https://github.com/senaite/senaite.core/pull/1027
 
-  - Reindex and recatalog of getDueDate for Analysis Requests
-    https://github.com/senaite/senaite.core/pull/1051
+- Reindex and recatalog of getDueDate for Analysis Requests
+  https://github.com/senaite/senaite.core/pull/1051
 
-  - Reindex of getDueDate for Analyses
-    https://github.com/senaite/senaite.core/pull/1032
+- Reindex of getDueDate for Analyses:
+  https://github.com/senaite/senaite.core/pull/1032
 
 - Workflow: `retract_ar` transition has been renamed to `invalidate`
   https://github.com/senaite/senaite.core/pull/1027

bika/__init__.py

@@ -1,9 +1,23 @@
-# This file is part of Bika LIMS
+# -*- coding: utf-8 -*-
 #
-# Copyright 2011-2016 by it's authors.
-# Some rights reserved. See LICENSE.txt, AUTHORS.txt.
+# This file is part of SENAITE.CORE.
+#
+# SENAITE.CORE is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, version 2.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program; if not, write to the Free Software Foundation, Inc., 51
+# Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# Copyright 2018-2019 by it's authors.
+# Some rights reserved, see README and LICENSE.
 
-# See http://peak.telecommunity.com/DevCenter/setuptools#namespace-packages
 try:
     __import__('pkg_resources').declare_namespace(__name__)
 except ImportError:

bika/lims/__init__.py

@@ -1,9 +1,22 @@
 # -*- coding: utf-8 -*-
 #
-# This file is part of SENAITE.CORE
+# This file is part of SENAITE.CORE.
 #
-# Copyright 2018 by it's authors.
-# Some rights reserved. See LICENSE.rst, CONTRIBUTORS.rst.
+# SENAITE.CORE is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, version 2.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program; if not, write to the Free Software Foundation, Inc., 51
+# Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# Copyright 2018-2019 by it's authors.
+# Some rights reserved, see README and LICENSE.
 
 import logging
 import warnings

bika/lims/adapters/__init__.py

@@ -1,6 +1,19 @@
 # -*- coding: utf-8 -*-
 #
-# This file is part of SENAITE.CORE
+# This file is part of SENAITE.CORE.
 #
-# Copyright 2018 by it's authors.
-# Some rights reserved. See LICENSE.rst, CONTRIBUTORS.rst.
+# SENAITE.CORE is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, version 2.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program; if not, write to the Free Software Foundation, Inc., 51
+# Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# Copyright 2018-2019 by it's authors.
+# Some rights reserved, see README and LICENSE.