docs: recommend --upgrade for all pip installations in a virtualenv

As suggested by Mads Kiilerich.

Don't recommend this practice when no virtualenv is used, i.e. root
installation or --user installation: in this case upgrading existing packages
may be too disruptive. The user can still add it manually if he so chooses.

docs/contributing.rst

@@ -1,314 +1,314 b''
 .. _contributing:
 
 =========================
 Contributing to Kallithea
 =========================
 
 Kallithea is developed and maintained by its users. Please join us and scratch
 your own itch.
 
 
 Infrastructure
 --------------
 
 The main repository is hosted on Our Own Kallithea (aka OOK) at
 https://kallithea-scm.org/repos/kallithea/, our self-hosted instance
 of Kallithea.
 
 For now, we use Bitbucket_ for `pull requests`_ and `issue tracking`_. The
 issue tracker is for tracking bugs, not for support, discussion, or ideas --
 please use the `mailing list`_ or :ref:`IRC <readme>` to reach the community.
 
 We use Weblate_ to translate the user interface messages into languages other
 than English. Join our project on `Hosted Weblate`_ to help us.
 To register, you can use your Bitbucket or GitHub account. See :ref:`translations`
 for more details.
 
 
 Getting started
 ---------------
 
 To get started with Kallithea development::
 
         hg clone https://kallithea-scm.org/repos/kallithea
         cd kallithea
         virtualenv ../kallithea-venv
         source ../kallithea-venv/bin/activate
         pip install --upgrade pip setuptools
-        pip install -e .
-        pip install -r dev_requirements.txt
+        pip install --upgrade -e .
+        pip install --upgrade -r dev_requirements.txt
         gearbox make-config my.ini
         gearbox setup-db -c my.ini --user=user --email=[e-mail] --password=password --repos=/tmp
         gearbox serve -c my.ini --reload &
         firefox http://127.0.0.1:5000/
 
 If you plan to use Bitbucket_ for sending contributions, you can also fork
 Kallithea on Bitbucket_ first (https://bitbucket.org/conservancy/kallithea) and
 then replace the clone step above by a clone of your fork. In this case, please
 see :ref:`contributing-guidelies` below for configuring your fork correctly.
 
 
 Contribution flow
 -----------------
 
 Starting from an existing Kallithea clone, make sure it is up to date with the
 latest upstream changes::
 
         hg pull
         hg update
 
 Review the :ref:`contributing-guidelines` and :ref:`coding-guidelines`.
 
 If you are new to Mercurial, refer to Mercurial `Quick Start`_ and `Beginners
 Guide`_ on the Mercurial wiki.
 
 Now, make some changes and test them (see :ref:`contributing-tests`). Don't
 forget to add new tests to cover new functionality or bug fixes.
 
 For documentation changes, run ``make html`` from the ``docs`` directory to
 generate the HTML result, then review them in your browser.
 
 Before submitting any changes, run the cleanup script::
 
         ./scripts/run-all-cleanup
 
 When you are completely ready, you can send your changes to the community for
 review and inclusion. Most commonly used methods are sending patches to the
 mailing list (via ``hg email``) or by creating a pull request on Bitbucket_.
 
 .. _contributing-tests:
 
 
 Running tests
 -------------
 
 After finishing your changes make sure all tests pass cleanly. Run the testsuite
 by invoking ``py.test`` from the project root::
 
     py.test
 
 Note that testing on Python 2.6 also requires ``unittest2``.
 
 Note that on unix systems, the temporary directory (``/tmp`` or where
 ``$TMPDIR`` points) must allow executable files; Git hooks must be executable,
 and the test suite creates repositories in the temporary directory. Linux
 systems with /tmp mounted noexec will thus fail.
 
 You can also use ``tox`` to run the tests with all supported Python versions
 (currently Python 2.6--2.7).
 
 When running tests, Kallithea uses `kallithea/tests/test.ini` and populates the
 SQLite database specified there.
 
 It is possible to avoid recreating the full test database on each invocation of
 the tests, thus eliminating the initial delay. To achieve this, run the tests as::
 
     gearbox serve -c kallithea/tests/test.ini --pid-file=test.pid --daemon
     KALLITHEA_WHOOSH_TEST_DISABLE=1 KALLITHEA_NO_TMP_PATH=1 py.test
     kill -9 $(cat test.pid)
 
 In these commands, the following variables are used::
 
     KALLITHEA_WHOOSH_TEST_DISABLE=1 - skip whoosh index building and tests
     KALLITHEA_NO_TMP_PATH=1 - disable new temp path for tests, used mostly for testing_vcs_operations
 
 You can run individual tests by specifying their path as argument to py.test.
 py.test also has many more options, see `py.test -h`. Some useful options
 are::
 
     -k EXPRESSION         only run tests which match the given substring
                           expression. An expression is a python evaluable
                           expression where all names are substring-matched
                           against test names and their parent classes. Example:
     -x, --exitfirst       exit instantly on first error or failed test.
     --lf                  rerun only the tests that failed at the last run (or
                           all if none failed)
     --ff                  run all tests but run the last failures first. This
                           may re-order tests and thus lead to repeated fixture
                           setup/teardown
     --pdb                 start the interactive Python debugger on errors.
     -s, --capture=no      don't capture stdout (any stdout output will be
                           printed immediately)
 
 Performance tests
 ^^^^^^^^^^^^^^^^^
 
 A number of performance tests are present in the test suite, but they are
 not run in a standard test run. These tests are useful to
 evaluate the impact of certain code changes with respect to performance.
 
 To run these tests::
 
     env TEST_PERFORMANCE=1 py.test kallithea/tests/performance
 
 To analyze performance, you could install pytest-profiling_, which enables the
 --profile and --profile-svg options to py.test.
 
 .. _pytest-profiling: https://github.com/manahl/pytest-plugins/tree/master/pytest-profiling
 
 .. _contributing-guidelines:
 
 
 Contribution guidelines
 -----------------------
 
 Kallithea is GPLv3 and we assume all contributions are made by the
 committer/contributor and under GPLv3 unless explicitly stated. We do care a
 lot about preservation of copyright and license information for existing code
 that is brought into the project.
 
 Contributions will be accepted in most formats -- such as pull requests on
 Bitbucket, something hosted on your own Kallithea instance, or patches sent by
 email to the `kallithea-general`_ mailing list.
 
 When contributing via Bitbucket, please make your fork of
 https://bitbucket.org/conservancy/kallithea/ `non-publishing`_ -- it is one of
 the settings on "Repository details" page. This ensures your commits are in
 "draft" phase and makes it easier for you to address feedback and for project
 maintainers to integrate your changes.
 
 .. _non-publishing: https://www.mercurial-scm.org/wiki/Phases#Publishing_Repository
 
 Make sure to test your changes both manually and with the automatic tests
 before posting.
 
 We care about quality and review and keeping a clean repository history. We
 might give feedback that requests polishing contributions until they are
 "perfect". We might also rebase and collapse and make minor adjustments to your
 changes when we apply them.
 
 We try to make sure we have consensus on the direction the project is taking.
 Everything non-sensitive should be discussed in public -- preferably on the
 mailing list.  We aim at having all non-trivial changes reviewed by at least
 one other core developer before pushing. Obvious non-controversial changes will
 be handled more casually.
 
 There is a main development branch ("default") which is generally stable so that
 it can be (and is) used in production. There is also a "stable" branch that is
 almost exclusively reserved for bug fixes or trivial changes. Experimental
 changes should live elsewhere (for example in a pull request) until they are
 ready.
 
 .. _coding-guidelines:
 
 
 Coding guidelines
 -----------------
 
 We don't have a formal coding/formatting standard. We are currently using a mix
 of Mercurial's (https://www.mercurial-scm.org/wiki/CodingStyle), pep8, and
 consistency with existing code. Run ``scripts/run-all-cleanup`` before
 committing to ensure some basic code formatting consistency.
 
 We support both Python 2.6.x and 2.7.x and nothing else. For now we don't care
 about Python 3 compatibility.
 
 We try to support the most common modern web browsers. IE9 is still supported
 to the extent it is feasible, IE8 is not.
 
 We primarily support Linux and OS X on the server side but Windows should also work.
 
 HTML templates should use 2 spaces for indentation ... but be pragmatic. We
 should use templates cleverly and avoid duplication. We should use reasonable
 semantic markup with element classes and IDs that can be used for styling and testing.
 We should only use inline styles in places where it really is semantic (such as
 ``display: none``).
 
 JavaScript must use ``;`` between/after statements. Indentation 4 spaces. Inline
 multiline functions should be indented two levels -- one for the ``()`` and one for
 ``{}``.
 Variables holding jQuery objects should be named with a leading ``$``.
 
 Commit messages should have a leading short line summarizing the changes. For
 bug fixes, put ``(Issue #123)`` at the end of this line.
 
 Use American English grammar and spelling overall. Use `English title case`_ for
 page titles, button labels, headers, and 'labels' for fields in forms.
 
 .. _English title case: https://en.wikipedia.org/wiki/Capitalization#Title_case
 
 Template helpers (that is, everything in ``kallithea.lib.helpers``)
 should only be referenced from templates. If you need to call a
 helper from the Python code, consider moving the function somewhere
 else (e.g. to the model).
 
 Notes on the SQLAlchemy session
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Each HTTP request runs inside an independent SQLAlchemy session (as well
 as in an independent database transaction). ``Session`` is the session manager
 and factory. ``Session()`` will create a new session on-demand or return the
 current session for the active thread. Many database operations are methods on
 such session instances - only ``Session.remove()`` should be called directly on
 the manager.
 
 Database model objects
 (almost) always belong to a particular SQLAlchemy session, which means
 that SQLAlchemy will ensure that they're kept in sync with the database
 (but also means that they cannot be shared across requests).
 
 Objects can be added to the session using ``Session().add``, but this is
 rarely needed:
 
 * When creating a database object by calling the constructor directly,
   it must explicitly be added to the session.
 
 * When creating an object using a factory function (like
   ``create_repo``), the returned object has already (by convention)
   been added to the session, and should not be added again.
 
 * When getting an object from the session (via ``Session().query`` or
   any of the utility functions that look up objects in the database),
   it's already part of the session, and should not be added again.
   SQLAlchemy monitors attribute modifications automatically for all
   objects it knows about and syncs them to the database.
 
 SQLAlchemy also flushes changes to the database automatically; manually
 calling ``Session().flush`` is usually only necessary when the Python
 code needs the database to assign an "auto-increment" primary key ID to
 a freshly created model object (before flushing, the ID attribute will
 be ``None``).
 
 TurboGears2 DebugBar
 ^^^^^^^^^^^^^^^^^^^^
 
 It is possible to enable the TurboGears2-provided DebugBar_, a toolbar overlayed
 over the Kallithea web interface, allowing you to see:
 
 * timing information of the current request, including profiling information
 * request data, including GET data, POST data, cookies, headers and environment
   variables
 * a list of executed database queries, including timing and result values
 
 DebugBar is only activated when ``debug = true`` is set in the configuration
 file. This is important, because the DebugBar toolbar will be visible for all
 users, and allow them to see information they should not be allowed to see. Like
 is anyway the case for ``debug = true``, do not use this in production!
 
 To enable DebugBar, install ``tgext.debugbar`` and ``kajiki`` (typically via
 ``pip``) and restart Kallithea (in debug mode).
 
 
 "Roadmap"
 ---------
 
 We do not have a road map but are waiting for your contributions. Refer to the
 wiki_ for some ideas of places we might want to go -- contributions in these
 areas are very welcome.
 
 
 Thank you for your contribution!
 --------------------------------
 
 
 .. _Weblate: http://weblate.org/
 .. _issue tracking: https://bitbucket.org/conservancy/kallithea/issues?status=new&status=open
 .. _pull requests: https://bitbucket.org/conservancy/kallithea/pull-requests
 .. _bitbucket: http://bitbucket.org/
 .. _mailing list: http://lists.sfconservancy.org/mailman/listinfo/kallithea-general
 .. _kallithea-general: http://lists.sfconservancy.org/mailman/listinfo/kallithea-general
 .. _Hosted Weblate: https://hosted.weblate.org/projects/kallithea/kallithea/
 .. _wiki: https://bitbucket.org/conservancy/kallithea/wiki/Home
 .. _DebugBar: https://github.com/TurboGears/tgext.debugbar
 .. _Quick Start: https://www.mercurial-scm.org/wiki/QuickStart
 .. _Beginners Guide: https://www.mercurial-scm.org/wiki/BeginnersGuides

docs/installation.rst

@@ -1,139 +1,139 b''
 .. _installation:
 
 ==========================
 Installation on Unix/Linux
 ==========================
 
 The following describes three different ways of installing Kallithea:
 
 - :ref:`installation-source`: The simplest way to keep the installation
   up-to-date and track any local customizations is to run directly from
   source in a Kallithea repository clone, preferably inside a virtualenv
   virtual Python environment.
 
 - :ref:`installation-virtualenv`: If you prefer to only use released versions
   of Kallithea, the recommended method is to install Kallithea in a virtual
   Python environment using `virtualenv`. The advantages of this method over
   direct installation is that Kallithea and its dependencies are completely
   contained inside the virtualenv (which also means you can have multiple
   installations side by side or remove it entirely by just removing the
   virtualenv directory) and does not require root privileges.
 
 - :ref:`installation-without-virtualenv`: The alternative method of installing
   a Kallithea release is using standard pip. The package will be installed in
   the same location as all other Python packages you have ever installed. As a
   result, removing it is not as straightforward as with a virtualenv, as you'd
   have to remove its dependencies manually and make sure that they are not
   needed by other packages.
 
 Regardless of the installation method you may need to make sure you have
 appropriate development packages installed, as installation of some of the
 Kallithea dependencies requires a working C compiler and libffi library
 headers. Depending on your configuration, you may also need to install
 Git and development packages for the database of your choice.
 
 For Debian and Ubuntu, the following command will ensure that a reasonable
 set of dependencies is installed::
 
     sudo apt-get install build-essential git python-pip python-virtualenv libffi-dev python-dev
 
 For Fedora and RHEL-derivatives, the following command will ensure that a
 reasonable set of dependencies is installed::
 
     sudo yum install gcc git python-pip python-virtualenv libffi-devel python-devel
 
 .. _installation-source:
 
 
 Installation from repository source
 -----------------------------------
 
 To install Kallithea in a virtualenv_ using the stable branch of the development
 repository, follow the instructions below::
 
         hg clone https://kallithea-scm.org/repos/kallithea -u stable
         cd kallithea
         virtualenv ../kallithea-venv
         . ../kallithea-venv/bin/activate
         pip install --upgrade pip setuptools
-        pip install -e .
+        pip install --upgrade -e .
         python2 setup.py compile_catalog   # for translation of the UI
 
 You can now proceed to :ref:`setup`.
 
 .. _installation-virtualenv:
 
 
 Installing a released version in a virtualenv
 ---------------------------------------------
 
 It is highly recommended to use a separate virtualenv_ for installing Kallithea.
 This way, all libraries required by Kallithea will be installed separately from your
 main Python installation and other applications and things will be less
 problematic when upgrading the system or Kallithea.
 An additional benefit of virtualenv_ is that it doesn't require root privileges.
 
 - Assuming you have installed virtualenv_, create a new virtual environment
   for example, in `/srv/kallithea/venv`, using the virtualenv command::
 
     virtualenv /srv/kallithea/venv
 
 - Activate the virtualenv_ in your current shell session and make sure the
   basic requirements are up-to-date by running::
 
     . /srv/kallithea/venv/bin/activate
     pip install --upgrade pip setuptools
 
 .. note:: You can't use UNIX ``sudo`` to source the ``virtualenv`` script; it
    will "activate" a shell that terminates immediately. It is also perfectly
    acceptable (and desirable) to create a virtualenv as a normal user.
 
 .. note:: Some dependencies are optional. If you need them, install them in
    the virtualenv too::
 
-     pip install psycopg2
-     pip install python-ldap
+     pip install --upgrade psycopg2
+     pip install --upgrade python-ldap
 
    This might require installation of development packages using your
    distribution's package manager.
 
 - Make a folder for Kallithea data files, and configuration somewhere on the
   filesystem. For example::
 
     mkdir /srv/kallithea
 
 - Go into the created directory and run this command to install Kallithea::
 
-    pip install kallithea
+    pip install --upgrade kallithea
 
   Alternatively, download a .tar.gz from http://pypi.python.org/pypi/Kallithea,
   extract it and run::
 
-    pip install .
+    pip install --upgrade .
 
 - This will install Kallithea together with all other required
   Python libraries into the activated virtualenv.
 
 You can now proceed to :ref:`setup`.
 
 .. _installation-without-virtualenv:
 
 
 Installing a released version without virtualenv
 ------------------------------------------------
 
 For installation without virtualenv, 'just' use::
 
     pip install kallithea
 
 Note that this method requires root privileges and will install packages
 globally without using the system's package manager.
 
 To install as a regular user in ``~/.local``, you can use::
 
     pip install --user kallithea
 
 You can now proceed to :ref:`setup`.
 
 
 .. _virtualenv: http://pypi.python.org/pypi/virtualenv

docs/upgrade.rst

@@ -1,185 +1,185 b''
 .. _upgrade:
 
 ===================
 Upgrading Kallithea
 ===================
 
 This describes the process for upgrading Kallithea, independently of the
 Kallithea installation method.
 
 .. note::
     If you are upgrading from a RhodeCode installation, you must first
     install Kallithea 0.3.2 and follow the instructions in the 0.3.2
     README to perform a one-time conversion of the database from
     RhodeCode to Kallithea, before upgrading to the latest version
     of Kallithea.
 
 
 1. Stop the Kallithea web application
 -------------------------------------
 
 This step depends entirely on the web server software used to serve
 Kallithea, but in any case, Kallithea should not be running during
 the upgrade.
 
 .. note::
     If you're using Celery, make sure you stop all instances during the
     upgrade.
 
 
 2. Create a backup of both database and configuration
 -----------------------------------------------------
 
 You are of course strongly recommended to make backups regularly, but it
 is *especially* important to make a full database and configuration
 backup before performing a Kallithea upgrade.
 
 Back up your configuration
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Make a copy of your Kallithea configuration (``.ini``) file.
 
 If you are using :ref:`rcextensions <customization>`, you should also
 make a copy of the entire ``rcextensions`` directory.
 
 Back up your database
 ^^^^^^^^^^^^^^^^^^^^^
 
 If using SQLite, simply make a copy of the Kallithea database (``.db``)
 file.
 
 If using PostgreSQL, please consult the documentation for the ``pg_dump``
 utility.
 
 If using MySQL, please consult the documentation for the ``mysqldump``
 utility.
 
 Look for ``sqlalchemy.url`` in your configuration file to determine
 database type, settings, location, etc.
 
 
 3. Activate the Kallithea virtual environment (if any)
 ------------------------------------------------------
 
 Verify that you are using the Python environment that you originally
 installed Kallithea in by running::
 
     pip freeze
 
 This will list all packages installed in the current environment. If
 Kallithea isn't listed, activate the correct virtual environment.
 See the appropriate installation page for details.
 
 
 4. Install new version of Kallithea
 -----------------------------------
 
 Please refer to the instructions for the installation method you
 originally used to install Kallithea.
 
 If you originally installed using pip, it is as simple as::
 
     pip install --upgrade kallithea
 
 If you originally installed from version control, it is as simple as::
 
     cd my-kallithea-clone
     hg pull -u
-    pip install -e .
+    pip install --upgrade -e .
 
 
 5. Upgrade your configuration
 -----------------------------
 
 Run the following command to create a new configuration (``.ini``) file::
 
     gearbox make-config new.ini
 
 Then compare it with your old config file and see what changed.
 
 .. note::
     Please always make sure your ``.ini`` files are up to date. Errors
     can often be caused by missing parameters added in new versions.
 
 .. _upgrade_db:
 
 
 6. Upgrade your database
 ------------------------
 
 .. note::
     If you are *downgrading* Kallithea, you should perform the database
     migration step *before* installing the older version. (That is,
     always perform migrations using the most recent of the two versions
     you're migrating between.)
 
 First, run the following command to see your current database version::
 
     alembic -c my.ini current
 
 Typical output will be something like "9358dc3d6828 (head)", which is
 the current Alembic database "revision ID". Write down the entire output
 for troubleshooting purposes.
 
 The output will be empty if you're upgrading from Kallithea 0.3.x or
 older. That's expected. If you get an error that the config file was not
 found or has no ``[alembic]`` section, see the next section.
 
 Next, if you are performing an *upgrade*: Run the following command to
 upgrade your database to the current Kallithea version::
 
     alembic -c my.ini upgrade head
 
 If you are performing a *downgrade*: Run the following command to
 downgrade your database to the given version::
 
     alembic -c my.ini downgrade 0.4
 
 Alembic will show the necessary migrations (if any) as it executes them.
 If no "ERROR" is displayed, the command was successful.
 
 Should an error occur, the database may be "stranded" half-way
 through the migration, and you should restore it from backup.
 
 Enabling old Kallithea config files for Alembic use
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Kallithea configuration files created before the introduction of Alembic
 (i.e. predating Kallithea 0.4) need to be updated for use with Alembic.
 Without this, Alembic will fail with an error like this::
 
     FAILED: No config file 'my.ini' found, or file has no '[alembic]' section
 
 If Alembic complains specifically about a missing ``alembic.ini``, it is
 likely because you did not specify a config file using the ``-c`` option.
 On the other hand, if the mentioned config file actually exists, you
 need to append the following lines to it::
 
     [alembic]
     script_location = kallithea:alembic
 
 Your config file should now work with Alembic.
 
 
 7. Rebuild the Whoosh full-text index
 -------------------------------------
 
 It is recommended that you rebuild the Whoosh index after upgrading since
 new Whoosh versions can introduce incompatible index changes.
 
 
 8. Start the Kallithea web application
 --------------------------------------
 
 This step once again depends entirely on the web server software used to
 serve Kallithea.
 
 Before starting the new version of Kallithea, you may find it helpful to
 clear out your log file so that new errors are readily apparent.
 
 .. note::
     If you're using Celery, make sure you restart all instances of it after
     upgrade.
 
 
 .. _virtualenv: http://pypi.python.org/pypi/virtualenv