Merge pull request #301 from NBISweden/release

First official release

.filebeat.yml

@@ -0,0 +1,13 @@
+filebeat:
+  prospectors:
+    -
+      paths:
+        - /home/travis/build/NBISweden/LocalEGA/tests/console.log
+      input_type: log
+      multiline:
+        pattern: '^\['
+        negate: true
+        match: after
+output:
+  logstash:
+    hosts: ["130.239.81.80:5600"]

.gitattributes

@@ -0,0 +1,3 @@
+*.rpm filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.tar.gz filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -3,10 +3,6 @@
 .DS_Store
 tmp/
 private/
-loggers/
-!src/lega/conf/loggers
-tests/
-storage
 
 # =====================================
 # Byte-compiled / optimized / DLL files
@@ -69,35 +65,14 @@ nosetests.xml
 coverage.xml
 *,cover
 .hypothesis/
+.pytest_cache
 
 # =====================================
 # Translations
 # =====================================
 *.mo
 *.pot
 
-# =====================================
-# Django stuff:
-# =====================================
-*.log
-local_settings.py
-
-# =====================================
-# Flask stuff:
-# =====================================
-instance/
-.webassets-cache
-
-# =====================================
-# Scrapy stuff:
-# =====================================
-.scrapy
-
-# =====================================
-# Sphinx documentation
-# =====================================
-docs/_build/
-
 # =====================================
 # PyBuilder
 # =====================================
@@ -112,29 +87,3 @@ target/
 # pyenv
 # =====================================
 .python-version
-
-# =====================================
-# celery beat schedule file
-# =====================================
-celerybeat-schedule
-
-# =====================================
-# dotenv
-# =====================================
-.env
-
-# =====================================
-# virtualenv
-# =====================================
-venv/
-ENV/
-
-# =====================================
-# Spyder project settings
-# =====================================
-.spyderproject
-
-# =====================================
-# Rope project settings
-# =====================================
-.ropeproject

.snyk

@@ -0,0 +1,2 @@
+language-settings:
+  python: "3.6"

.travis.yml

@@ -0,0 +1,42 @@
+language: python
+
+python: 3.6
+
+services: docker
+
+# command to install dependencies
+
+stages:
+  - name: unit_tests
+    if: type IN (push, pull_request)
+  - name: integration_tests
+    if: type IN (pull_request)
+
+jobs:
+  include:
+    - stage: unit_tests
+      python: 3.6
+      before_script:
+        - pip install tox-travis
+      # command to run tests
+      script: tox
+    - stage: integration_tests
+      before_script:
+        # https://elk-docker.readthedocs.io/#es-not-starting-max-map-count
+        # mostly used by ELK stack; Solving issue #252
+        # - sudo sysctl -w vm.max_map_count=262144
+        - cd deployments/docker
+        - make bootstrap
+        - sudo chown -R travis private
+        - docker network create cega
+        - docker-compose up -d ${DOCKER_CONTAINERS}
+        - docker-compose ps
+      script:
+        - sleep 10
+        - cd tests
+        - mvn test -B
+
+notifications:
+  email: false
+  slack:
+    secure: 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

CONTRIBUTING.rst

@@ -0,0 +1,173 @@
+.. role:: bolditalic
+    :class: bolditalic
+
+=======================
+Contributing guidelines
+=======================
+
+We thank you in advance |thumbup| |tada| for taking the time to
+contribute, whether with *code* or with *ideas*, to the Local EGA
+project.
+
+------------------------
+AGILE project management
+------------------------
+
+We use *Zenhub*, the Agile project management within Github.
+
+You should first `install it`_ if you want to contribute or just follow the project progress.  
+You can also use the `Zenhub app`_ if you wish.
+
+In short, the `AGILE method`_ helps developers organize themselves:
+
+* They decide about the tasks (not the managers)
+* Main Tasks should be divided into smaller manageable ones. The big
+  tasks are called *Epics*.
+* We have a given period (called Sprint) to work on a chosen
+  task. Here, a Sprint spans across 2 weeks.
+* We review the work done at the end of the Sprint, closing issues or
+  pushing them into the next Sprint. Ideally, they are sub-divided in
+  case they encounter obstacles.
+* We have a short meeting every weekday at 9:30 AM. We call it a
+  *standup* and we use it to keep everyone on point, and identify
+  quickly blockers. It's not a lengthy discussion. We ask:
+
+  - What did you get done yesterday (or last week, last month, etc.)?
+  - What are you working on now?
+  - What isn’t going well, and on what could you use help?
+
+---------
+Procedure
+---------
+
+1. Create an issue on Github, and talk to the team members on the NBIS
+   local-ega Slack channel. You can alternatively pick one already
+   created.
+
+.. note:: 
+   Contact `Jonas Hagberg`_ to request access if you are not part of that channel already.
+
+
+2. Assign yourself to that issue.
+
+#. Discussions on how to proceed about that issue take place in the
+   comment section on that issue, beforehand.  
+
+   The keyword here is *beforehand*. It is usually a good idea to talk
+   about it first. Somebody might have already some pieces in place,
+   we avoid unnecessary work duplication and a waste of time and
+   effort.
+
+#. Work on it (on a fork, or on a separate branch) as you wish. That's
+   what ``git`` is good for. This GitHub repository follows
+   the `coding guidelines from NBIS`_.
+
+   Name your branch as you wish and prefix the name with:
+
+   * ``feature/`` if it is a code feature
+   * ``hotfix/`` if you are fixing an urgent bug
+
+   Use comments in your code, choose variable and function names that
+   clearly show what you intend to implement.
+
+   Use `git rebase -i`_ in
+   order to rewrite your history, and have meaningful commits.  That
+   way, we avoid the 'Typo', 'Work In Progress (WIP)', or
+   'Oops...forgot this or that' commits.
+
+   Limit the first line of your git commits to 72 characters or less.
+
+
+#. Create a Pull Request (PR), so that your code is reviewed by the
+   admins on this repository.  
+
+   That PR should be connected to the issue you are working on.
+   Moreover, the PR:
+
+   - should use ``Estimate=1``,
+   - should be connected to:
+
+     * an ``Epic``,
+     * a ``Milestone`` and
+     * a ``User story``
+     * ... or several.
+
+   N.B: Pull requests are done to the ``dev`` branch. PRs to ``master`` are rejected.
+
+#. Selecting a review goes as follows: Pick one *main* reviewer.  It
+   is usually one that you had discussions with, and is somehow 
+   connected to that issue. If this is not the case, pick several reviewers.
+
+   Note that, in turn, the main reviewer might ask another reviewer
+   for help. The approval of all reviewers is compulsory in order to
+   merge the PR. Moreover, the main reviewer is the one merging the
+   PR, not you.
+
+   Find more information on the `NBIS reviewing guidelines`_.
+
+
+#. It is possible that your PR requires changes (because it creates
+   conflicts, doesn't pass the integrated tests or because some parts
+   should be rewritten in a cleaner manner, or because it does not
+   follow the standards, or you're requesting the wrong branch to pull
+   your code, etc...) In that case, a reviewer will request changes
+   and describe them in the comment section of the PR.
+
+   You then update your branch with new commits. We will see the PR
+   changes faster if you ping the reviewer in the slack channel.
+
+   Note that the comments *in the PR* are not used to discuss the
+   *how* and *why* of that issue. These discussions are not about the
+   issue itself but about *a solution* to that issue.
+
+   Recall that discussions about the issue are good and prevent
+   duplicated or wasted efforts, but they take place in the comment
+   section of the related issue (see point 4), not in the PR.
+
+   Essentially, we don't want to open discussions when the work is
+   done, and there is no recourse, such that it's either accept or
+   reject. We think we can do better than that, and introduce a finer
+   grained acceptance, by involving *beforehand* discussions so that
+   everyone is on point.
+
+
+
+-------------------
+Did you find a bug?
+-------------------
+
+* Ensure that the bug was not already reported by `searching under Issues`_.
+
+* Do :bolditalic:`not` file it as a plain GitHub issue (we use the
+  issue system for our internal tasks (see Zenhub)).  If you're unable
+  to find an (open) issue addressing the problem, `open a new one`_.
+  Be sure to prefix the issue title with **[BUG]** and to include:
+
+  - a *clear* description,
+  - as much relevant information as possible, and 
+  - a *code sample* or an (executable) *test case* demonstrating the expected behaviour that is not occurring.
+
+* If possible, use the following `template to report a bug`_.
+
+.. todo:: Make that template
+
+
+----
+
+| Thanks again,  
+| /NBIS System Developers
+
+.. _Zenhub: https://www.zenhub.com
+.. _install it: https://www.zenhub.com/extension
+.. _Zenhub app: https://app.zenhub.com
+.. _AGILE method: https://www.zenhub.com/blog/how-to-use-github-agile-project-management
+.. _Jonas Hagberg: https://nbis.se/about/staff/jonas-hagberg/
+.. _coding guidelines from NBIS: https://github.com/NBISweden/development-guidelines
+.. _git rebase -i: https://git-scm.com/book/en/v2/Git-Tools-Rewriting-History
+.. _NBIS reviewing guidelines: https://github.com/NBISweden/development-guidelines#how-we-do-code-reviews
+.. _searching under Issues: https://github.com/NBISweden/LocalEGA/issues?utf8=%E2%9C%93&q=is%3Aissue%20label%3Abug%20%5BBUG%5D%20in%3Atitle
+.. _open a new one: https://github.com/NBISweden/LocalEGA/issues/new?title=%5BBUG%5D
+.. _template to report a bug: todo
+.. |tada| unicode:: U+1f389
+.. |thumbup| unicode:: U+1f44d
+