feat: check for Git in relevant commands and put this requirement in …

…the docs

* docs: add git requirement to memote isntall instruction

* feat: check for the presence of git in all relevant CLI commands

* chore: update changelog

* chore: implement suggestions from code review

HISTORY.rst

@@ -3,6 +3,8 @@ History
 
 Next Release
 ------------
+* Include memote's requirement for git on installation instructions.
+* Check for the presence of `git` in CLI commands that require it.
 * Replace vega with taucharts in all reports.
 * Fix plots to be large enough.
 * Fix responsive behaviour. 

README.rst

@@ -58,15 +58,19 @@ at via GitHub pages for your repository.
 Installation
 ============
 
-We highly recommend creating a Python virtualenv for your model testing purposes.
+Before installing `memote`, make sure that you have correctly installed the
+latest version of `git <https://git-scm.com/>`_.
 
-To install memote, run this command in your terminal:
+Moreover, we highly recommend creating a Python virtualenv for your model
+testing purposes.
+
+To install `memote`, run this command in your terminal:
 
 .. code-block:: console
 
     $ pip install memote
 
-This is the preferred method to install memote, as it will always install the
+This is the preferred method to install `memote`, as it will always install the
 most recent stable release.
 
 .. who-start
@@ -99,7 +103,7 @@ Credits
 This package was created with Cookiecutter_ and the
 `audreyr/cookiecutter-pypackage`_ project template.
 
-Memote relies on click_ for the command line interface, pytest_ for unit 
+`Memote` relies on click_ for the command line interface, pytest_ for unit
 and model tests, gitpython_ for interacting with git repositories, 
 pandas_ for tabular datastructures and data input, jinja2_ for interacting 
 with HTML templates, cobrapy_ for analysing genome-scale metabolic 
@@ -116,7 +120,7 @@ The Memote Report App user interface is built with `Angular 5`_,
 `Angular Flex-Layout`_, and `Angular Material`_. We rely on Vega_ for plotting 
 results.
 
-The initial development of memote has received funding from:
+The initial development of `memote` has received funding from:
 
 .. image:: https://upload.wikimedia.org/wikipedia/commons/d/d5/Novo_nordisk_foundation_Logo.png
         :target: http://novonordiskfonden.dk/en

docs/installation.rst

@@ -4,10 +4,14 @@
 Installation
 ============
 
+Before installing memote, make sure that you have correctly installed the
+latest version of `git`_.
+
 We highly recommend creating a Python `virtualenv`_ for your model testing
 purposes.
 
 .. _virtualenv: http://docs.python-guide.org/en/latest/dev/virtualenvs/
+.. _git: https://git-scm.com/
 
 Stable release
 --------------

memote/suite/cli/callbacks.py

@@ -22,6 +22,7 @@
 import shlex
 import sys
 import logging
+from subprocess import check_output, CalledProcessError
 
 import click
 import git
@@ -97,3 +98,18 @@ def abort_if_false(ctx, param, value):
     """Require confirmation."""
     if not value:
         ctx.abort()
+
+
+def git_installed():
+    """Interrupt execution of memote if `git` has not been installed."""
+    LOGGER.info("Checking `git` installation.")
+    try:
+        check_output(['git', '--version'])
+    except CalledProcessError as e:
+        LOGGER.critical(
+            "The execution of memote was interrupted since no installation of "
+            "`git` could be detected. Please install git to use "
+            "this functionality: "
+            "https://git-scm.com/book/en/v2/Getting-Started-Installing-Git")
+        LOGGER.debug("Underlying error:", exc_info=e)
+        sys.exit(1)

memote/suite/cli/reports.py

@@ -143,6 +143,7 @@ def snapshot(model, filename, pytest_args, exclusive, skip, solver,
                    "option can be specified multiple times.")
 def history(location, model, filename, deployment, custom_config):
     """Generate a report over a model's git commit history."""
+    callbacks.git_installed()
     LOGGER.info("Initialising history report generation.")
     if location is None:
         raise click.BadParameter("No 'location' given or configured.")

memote/suite/cli/runner.py

@@ -147,6 +147,7 @@ def is_verbose(arg):
     if ignore_git:
         repo = None
     else:
+        callbacks.git_installed()
         repo = callbacks.probe_git()
     if collect:
         if repo is not None:
@@ -239,6 +240,7 @@ def new(directory, replay):
     --directory option.
 
     """
+    callbacks.git_installed()
     if directory is None:
         directory = os.getcwd()
     cookiecutter("gh:opencobra/cookiecutter-memote", output_dir=directory,
@@ -324,6 +326,7 @@ def history(model, message, rewrite, solver, location, pytest_args, deployment,
 
     """
     # callbacks.validate_path(model)
+    callbacks.git_installed()
     if location is None:
         raise click.BadParameter("No 'location' given or configured.")
     if "--tb" not in pytest_args:
@@ -730,6 +733,7 @@ def _setup_travis_ci(gh_repo_name, auth_token, repo_access_token):
               help="The GitHub username. Usually this is configured for you.")
 def online(note, github_repository, github_username):
     """Upload the repository to GitHub and enable testing on Travis CI."""
+    callbacks.git_installed()
     try:
         repo = git.Repo()
     except git.InvalidGitRepositoryError: