diff --git a/AUTHORS b/AUTHORS
index 7236e8939d41be4157e063796c475fd62341e96c..81d02020d8d83361bb7a7c64569504440d643466 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1,5 +1,8 @@
Leiden University Medical Center department of Human Genetics <humgen@lumc.nl>
Jeroen Laros <j.f.j.laros@lumc.nl>
-Gerben Stouten
+Martijn Vermaat <martijn@vermaat.name>
+Jonathan Vis <jvis@liacs.nl>
+Gerben Stouten <gstouten@gmail.com>
Gerard Schaafsma <g.c.p.schaafsma@lumc.nl>
-Martijn Vermaat <m.vermaat.hg@lumc.nl>
+Daria Dvorkina <dasha@dvorkina.ru>
+Alisa Muraveva <alisa391213725@yandex.ru>
diff --git a/README b/DEVELOPMENT.md
similarity index 68%
rename from README
rename to DEVELOPMENT.md
index 9b32aa2f769bb4d9e5373bb5f37ddc6c4e3fa8cc..b62dbd47965dc144231af40b3e3224f9ec99a11b 100644
--- a/README
+++ b/DEVELOPMENT.md
@@ -1,19 +1,16 @@
-Mutalyzer, a HGVS variant nomenclature checker
-==============================================
+Mutalyzer development
+=====================
+Development of Mutalyzer happens on the GitLab server:
+https://git.lumc.nl/mutalyzer/mutalyzer
-Documentation
--------------
-See the doc/ directory for (possibly outdated) developer documentation and
-presentation slides related to Mutalyzer. See http://www.mutalyzer.nl for
-user documentation.
-
-
-Installation
+Coding style
------------
-See the INSTALL file for installation instructions.
+In general, try to follow the [PEP 8](http://www.python.org/dev/peps/pep-0008)
+guidelines for Python code and
+[PEP 257](http://www.python.org/dev/peps/pep-0257/) for docstrings.
Unit tests
@@ -34,85 +31,76 @@ Or, if you are in a hurry, skip the long-running tests with:
MUTALYZER_ENV=test MUTALYZER_QUICK_TEST=1 nosetests -v
-Release management
-------------------
+Working with feature branches
+-----------------------------
-The current Mutalyzer version is recorded in `mutalyzer/__init__.py`. See the
-comments in that file for more info of the versioning scheme.
+New features are best implemented in their own branches, isolating the work
+from unrelated developments. In fact, it's good practice to **never work
+directly on the master branch** but always in a separate branch. For this
+reason, the master branch on the GitLab server is locked. Feature branches can
+be merged back into master via a **merge request** in GitLab.
-On the event of a new release, the following is done:
+Before starting work on your feature, create a branch for it:
- emacs mutalyzer/__init__.py
+ git checkout -b your-feature
-Update `__date__`, remove `'dev'` from `__version_info__` and set `RELEASE` to
-`True`.
+Commit changes on this branch. If you're happy with it, push to GitLab:
- svn commit -m 'Release 2.0.beta-11'
- svn cp https://humgenprojects.lumc.nl/svn/mutalyzer/trunk \
- https://humgenprojects.lumc.nl/svn/mutalyzer/tags/mutalyzer-2.0.beta-11 \
- -m 'Tag 2.0.beta-11'
- emacs mutalyzer/__init__.py
+ git push origin your-feature -u
-Set `__version_info__` to a new version ending with `'dev'` and set `RELEASE`
-to `FALSE`.
+Now create a merge request to discuss the implementation with your
+colleagues. This might involve adding additional commits which are included in
+the merge request by pushing your branch again:
- svn commit -m 'Open development for 2.0.beta-12'
-
-Be sure to upgrade your installations to the new version as described in the
-INSTALL file (e.g. `sudo python setup.py develop` for development checkouts).
+ git commit
+ git push
+You may also be asked to rebase your branch on the master branch if it has
+changed since you started your work. This will require a forced push:
-Working with feature branches
------------------------------
+ git fetch
+ git rebase origin/master
+ git push -f
-Some features are best developed isolated in a separate branch (a 'feature
-branch') before being merged into trunk. To make it easier to switch between
-branches, don't checkout the entire repository tree from its root. Instead,
-checkout the branch subdirectory (or trunk) directly and use `svn switch` to
-switch between them. Otherwise, you might need to update you Apache config and
-run `sudo python setup.py develop` every time you switch branches.
+If the work is done, a developer can merge your branch and close the merge
+request. After the branch was merged you can safely delete it:
-To create the branch from current trunk:
+ git branch -d your-feature
- svn cp https://humgenprojects.lumc.nl/svn/mutalyzer/trunk \
- https://humgenprojects.lumc.nl/svn/mutalyzer/branches/my-feature-branch \
- -m 'Create my-feature-branch from trunk'
-To work from this branch, switch your checkout to there:
+Release management
+------------------
- svn switch https://humgenprojects.lumc.nl/svn/mutalyzer/branches/my-feature-branch
+The current Mutalyzer version is recorded in `mutalyzer/__init__.py`. See the
+comments in that file for more info of the versioning scheme.
-To make it easier to reintegrate long-running branches, you can periodically
-merge trunk into them:
+On the event of a new release, the following is done:
- svn merge https://humgenprojects.lumc.nl/svn/mutalyzer/trunk
+ emacs mutalyzer/__init__.py
-Use `mergeinfo` to see which revisions are already merged. You can cherry-pick
-revisions to merge by using the `-c` option:
+Update `__date__`, remove `dev` from `__version_info__` and set `RELEASE` to
+`True`.
- svn mergeinfo https://humgenprojects.lumc.nl/svn/mutalyzer/trunk \
- --show-revs eligible
- svn merge -c 354 https://humgenprojects.lumc.nl/svn/mutalyzer/trunk
+ git commit -am 'Bump version to 2.0.beta-XX'
+ git tag -a 'mutalyzer-2.0.beta-XX'
+ git push --tags
-If you just want to mark a revision as being merged, you can use the
-`--record-only` switch.
+ emacs mutalyzer/__init__.py
-Reintegrating a branch into trunk is done from the trunk checkout:
+Set `__version_info__` to a new version ending with `'dev'` and set `RELEASE`
+to `FALSE`.
- svn switch https://humgenprojects.lumc.nl/svn/mutalyzer/trunk
- svn merge --reintegrate \
- https://humgenprojects.lumc.nl/svn/mutalyzer/branches/my-feature-branch
- svn rm https://humgenprojects.lumc.nl/svn/mutalyzer/branches/my-feature-branch \
- -m 'Delete refactor-mutalyzer-branch'
+ git commit -am 'Open development for 2.0.beta-YY'
-All `merge` operations taken an optional `--dry-run` switch. Use it to see
-what would happen without having to actually applying.
+Be sure to upgrade your installations to the new version as described in the
+INSTALL file (e.g. `sudo python setup.py develop` for development checkouts).
Development notes
-----------------
Todo list:
+
- Improve the web interface design :)
- Test all uses of mkstemp().
- Use naming conventions for modules Crossmap, Db, File, GenRecord, Retriever
@@ -154,6 +142,7 @@ Todo list:
- Be more explicit in all the type of descriptions we don't currently support.
Code style guide:
+
- Follow PEP 8 (code) and PEP 257 (docstrings).
http://www.python.org/dev/peps/pep-0008/
http://www.python.org/dev/peps/pep-0257/
@@ -174,6 +163,7 @@ Code style guide:
effort.
Obsoleted features:
+
- On eu.liacs.nl:
/etc/apache2/mods-enabled/rewrite.load contains a rewrite rule that converts
"Variant_info.php" to "Variant_info".
@@ -188,6 +178,7 @@ Dependencies
------------
Mutalyzer depends on the following (Debian/Ubuntu) packages:
+
- mysql-server >= 5.1
- python >= 2.6
- python-mysqldb >= 1.2.2
@@ -202,6 +193,7 @@ Mutalyzer depends on the following (Debian/Ubuntu) packages:
- python-suds >= 0.3.9-1
The web and SOAP interfaces depend on the following packages:
+
- apache2 >= 2.2.11
- libapache2-mod-wsgi >= 2.8
- python-webpy >= 0.33
@@ -209,9 +201,11 @@ The web and SOAP interfaces depend on the following packages:
- python-simpletal >= 4.1-6
Automatic remote deployment depends on Fabric:
+
- fabric >= 0.9.0-2
The unit tests depend on the following packages:
+
- python-nose >= 0.11
- python-webtest >= 1.2.3
diff --git a/INSTALL b/INSTALL.md
similarity index 96%
rename from INSTALL
rename to INSTALL.md
index fe72b61625073c44d66ed1aa91bfff68513fe557..b74fc19a2839f53055434f26da4b83efba601fe2 100644
--- a/INSTALL
+++ b/INSTALL.md
@@ -39,7 +39,8 @@ Short version
Run the following commands:
- svn co https://www.mutalyzer.nl/svn/mutalyzer2/trunk .
+ git clone https://git.lumc.nl/mutalyzer/mutalyzer
+ cd mutalyzer
sudo bash extras/pre-install.sh
sudo python setup.py install
sudo bash extras/post-install.sh
@@ -76,9 +77,9 @@ your hands on a tarball and:
tar -zxvf mutalyzer-XXX.tar.gz
cd mutalyzer-XXX
-Or get the source from SVN directly:
+Or get the source from GitLab directly:
- svn https://www.mutalyzer.nl/svn/mutalyzer2/trunk mutalyzer
+ git clone https://git.lumc.nl/mutalyzer/mutalyzer
cd mutalyzer
diff --git a/README.md b/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..334fd4a5a08584bda0e05086b3accdaac73962d3
--- /dev/null
+++ b/README.md
@@ -0,0 +1,26 @@
+Mutalyzer, an HGVS variant nomenclature checker
+===============================================
+
+The canonical Mutalyzer installation can be found at https://mutalyzer.nl
+
+
+Documentation and issue tracker
+-------------------------------
+
+See the doc directory for (possibly outdated) developer documentation and
+presentation slides related to Mutalyzer. See the
+[Mutalyzer Trac](https://humgenprojects.lumc.nl/trac/mutalyzer) for user
+documentation and issue tracker.
+
+
+Installation
+------------
+
+See the INSTALL.md file for installation instructions.
+
+
+Development
+-----------
+
+The DEVELOPMENT.md file has more information for developers working on
+Mutalyzer.