Replace travis with github actions (#729)

* refactor: replace travis with github actions * enhance: use deployment branch from configuration at memote online * fix: use the actual deployment branch on memote online * test: remove travis_ci from tests * docs: add new entries to next release * refactor: remove github username from online Since it is now Github's token dependant * docs: write down user documentation for GH token * fix: create deployment branch if it does not exist * test: print debug information on failing the CLI command * test: add a mock github token for testing * chore: drop support for python3.6/7 in favor of pyhon3.9/10 Since python3.6 is deprecated and python3.7 has dependencies with unresolvable security issues (no longer supported). * style: flake8 * docs: update HISTORY.rst Co-authored-by: Moritz E. Beber <[email protected]> * chore: point `memote new` back to to the upstream cookiecutter --------- Co-authored-by: Moritz E. Beber <[email protected]>
opencobra · Sep 18, 2023 · 4c08f46 · 4c08f46
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -4,6 +4,12 @@ History
 Next Release
 ------------
 
+* Fix ``memote online``, given breaking changes in Github Authentication.
+* Replace travis-CI with github actions.
+* (Cookiecutter) Add an action for comparing models in Pull
+  Requests (`#23 <https://github.com/opencobra/cookiecutter-memote/pull/23>`_).
+* Dropped support for python3.6 and python3.7 in favor of python3.8 to python3.11.
+
 0.14.0 (2023-09-13)
 -------------------
 * Fix problems with the deprecated API of ``importlib_resources``. Update to either use

diff --git a/docs/getting_started.rst b/docs/getting_started.rst
@@ -146,19 +146,18 @@ results and report are stored on the deployment branch (typically the
 ``gh-pages`` branch).
 
 
-In order to make your local git repository available online and enable continuous integration via Travis CI, you can run:
+In order to make your local git repository available online and enable continuous integration via Github Actions, you can run:
 
 .. code-block:: console
 
-    $ memote online
+    $ memote online --token "your-github-token"
 
-This will use require your GitHub password to create the repository, connect it
-with Travis CI, and generate a GitHub token to be used for continuous
-integration of the history report.
+This requires setting a token on Github (see `GitHub documentation`_) and providing it as 
+the ``--token`` argument. Alternatively, an environment variable ``GITHUB_TOKEN`` can be set to avoid writing the token in the command line.
 
 Now, after each edit to the model in the repository, the user can generate
 an update to the continuous model report shown at the project's gh-pages
-branch. That means each commit should be pushed to Travis individually.
+branch. That means each commit should be pushed individually.
 
 The continuous report will look like this:
 
@@ -227,6 +226,7 @@ history report in your repository, you can run ``memote report history`` from
 any branch at any time to generate it.
 
 .. _GitHub: https://github.com
+.. _GitHub documentation: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token
 .. _GitLab: https://gitlab.com
 
 *******************************************************************************

diff --git a/setup.cfg b/setup.cfg
@@ -45,12 +45,12 @@ install_requires =
 	future
 	pytest >=4.0
 	gitpython
+	PyGithub ~= 1.55
 	pandas
 	Jinja2
 	cookiecutter
 	cobra >=0.17
 	ruamel.yaml >=0.15
-	travis-encrypt<1.2.0
 	sympy
 	sqlalchemy
 	requests

diff --git a/src/memote/suite/cli/callbacks.py b/src/memote/suite/cli/callbacks.py
@@ -66,12 +66,16 @@ def validate_repository(context, param, value):
         raise click.BadParameter("No GitHub repository slug provided or configured.")
 
 
-def validate_username(context, param, value):
-    """Load username from different locations."""
+def validate_token(context, param, value):
+    """Verify that a token was provided, pointing to documentation."""
     if value is not None:
         return value
     else:
-        raise click.BadParameter("No GitHub username provided or configured.")
+        raise click.BadParameter(
+            "No GitHub token provided. See https://memote.readthedocs.io/en/"
+            "latest/getting_started.html#ci-tested-online-and-public-workflow"
+            " for instructions on how to set it up."
+        )
 
 
 def probe_git():