Update test suite to remove unittest dependency in favor of pytest (feature/pytest)

docs/_static/custom.css

@@ -30,62 +30,54 @@ body.light-theme {
     background-color: blue !important;
 }
 
-pre.light-theme .kn { color: #2838b0 !important } /* Keyword.Namespace */
-pre.light-theme .kp { color: #2838b0 !important } /* Keyword.Pseudo */
-pre.light-theme .kr { color: #2838b0 !important } /* Keyword.Reserved */
-pre.light-theme .kt { color: #2838b0; font-style: italic !important } /* Keyword.Type */
-pre.light-theme .m { color: #444444 !important } /* Literal.Number */
-pre.light-theme .s { color: #b83838 !important } /* Literal.String */
-pre.light-theme .na { color: #388038 !important } /* Name.Attribute */
-pre.light-theme .nb { color: #388038 !important } /* Name.Builtin */
-pre.light-theme .nc { color: #287088 !important } /* Name.Class */
-pre.light-theme .no { color: #b85820 !important } /* Name.Constant */
-pre.light-theme .nd { color: #287088 !important } /* Name.Decorator */
-pre.light-theme .ni { color: #709030 !important } /* Name.Entity */
-pre.light-theme .ne { color: #908828 !important } /* Name.Exception */
-pre.light-theme .nf { color: #785840 !important } /* Name.Function */
-pre.light-theme .nl { color: #289870 !important } /* Name.Label */
-pre.light-theme .nn { color: #289870 !important } /* Name.Namespace */
-pre.light-theme .nt { color: #2838b0 !important } /* Name.Tag */
-pre.light-theme .nv { color: #b04040 !important } /* Name.Variable */
-pre.light-theme .ow { color: #a848a8 !important } /* Operator.Word */
-pre.light-theme .pm { color: #888888 !important } /* Punctuation.Marker */
-pre.light-theme .w { color: #a89028 !important } /* Text.Whitespace */
-pre.light-theme .mb { color: #444444 !important } /* Literal.Number.Bin */
-pre.light-theme .mf { color: #444444 !important } /* Literal.Number.Float */
-pre.light-theme .mh { color: #444444 !important } /* Literal.Number.Hex */
-pre.light-theme .mi { color: #444444 !important } /* Literal.Number.Integer */
-pre.light-theme .mo { color: #444444 !important } /* Literal.Number.Oct */
-pre.light-theme .sa { color: #444444 !important } /* Literal.String.Affix */
-pre.light-theme .sb { color: #b83838 !important } /* Literal.String.Backtick */
-pre.light-theme .sc { color: #a848a8 !important } /* Literal.String.Char */
-pre.light-theme .dl { color: #b85820 !important } /* Literal.String.Delimiter */
-pre.light-theme .sd { color: #b85820; font-style: italic !important } /* Literal.String.Doc */
-pre.light-theme .s2 { color: #b83838 !important } /* Literal.String.Double */
-pre.light-theme .se { color: #709030 !important } /* Literal.String.Escape */
-pre.light-theme .sh { color: #b83838 !important } /* Literal.String.Heredoc */
-pre.light-theme .si { color: #b83838; text-decoration: underline !important } /* Literal.String.Interpol */
-pre.light-theme .sx { color: #a848a8 !important } /* Literal.String.Other */
-pre.light-theme .sr { color: #a848a8 !important } /* Literal.String.Regex */
-pre.light-theme .s1 { color: #b83838 !important } /* Literal.String.Single */
-pre.light-theme .ss { color: #b83838 !important } /* Literal.String.Symbol */
-pre.light-theme .bp { color: #388038; font-style: italic !important } /* Name.Builtin.Pseudo */
-pre.light-theme .fm { color: #b85820 !important } /* Name.Function.Magic */
-pre.light-theme .vc { color: #b04040 !important } /* Name.Variable.Class */
-pre.light-theme .vg { color: #908828 !important } /* Name.Variable.Global */
-pre.light-theme .vi { color: #b04040 !important } /* Name.Variable.Instance */
-pre.light-theme .vm { color: #b85820 !important } /* Name.Variable.Magic */
-pre.light-theme .il { color: #444444 !important } /* Literal.Number.Integer.Long */
-pre.light-theme .n { color: #444444 !important } /* Misc */
-pre.light-theme .o { color: #444 !important } /* Misc */
-pre.light-theme .p { color: #444 !important } /* Misc */
-pre.light-theme .k { color: #a848a8 !important } /* Misc */
-pre.light-theme .kc { color: #2838b0 !important } /* Misc */
-pre.light-theme .go { color: #546E7A !important } /* Misc */
-pre.light-theme .go { color: #546E7A !important } /* Misc */
-pre.light-theme .c1 { color: #546E7A !important } /* Misc */
-pre.light-theme .copy { background: #BBB !important } /* Misc */
-
-
-.c1 { color: #EEFFFF !important } /* Misc */
-.go { color: #EEFFFF !important } /* Misc */
+pre.light-theme .kn { color: #2838b0 !important} /* Keyword.Namespace */
+pre.light-theme .kp { color: #2838b0 !important} /* Keyword.Pseudo */
+pre.light-theme .kr { color: #2838b0 !important} /* Keyword.Reserved */
+pre.light-theme .kt { color: #2838b0; font-style: italic !important} /* Keyword.Type */
+pre.light-theme .m { color: #444444 !important} /* Literal.Number */
+pre.light-theme .s { color: #b83838 !important} /* Literal.String */
+pre.light-theme .na { color: #388038 !important} /* Name.Attribute */
+pre.light-theme .nb { color: #388038 !important} /* Name.Builtin */
+pre.light-theme .nc { color: #287088 !important} /* Name.Class */
+pre.light-theme .no { color: #b85820 !important} /* Name.Constant */
+pre.light-theme .nd { color: #287088 !important} /* Name.Decorator */
+pre.light-theme .ni { color: #709030 !important} /* Name.Entity */
+pre.light-theme .ne { color: #908828 !important} /* Name.Exception */
+pre.light-theme .nf { color: #785840 !important} /* Name.Function */
+pre.light-theme .nl { color: #289870 !important} /* Name.Label */
+pre.light-theme .nn { color: #289870 !important} /* Name.Namespace */
+pre.light-theme .nt { color: #2838b0 !important} /* Name.Tag */
+pre.light-theme .nv { color: #b04040 !important} /* Name.Variable */
+pre.light-theme .ow { color: #a848a8 !important} /* Operator.Word */
+pre.light-theme .pm { color: #888888 !important} /* Punctuation.Marker */
+pre.light-theme .w { color: #a89028 !important} /* Text.Whitespace */
+pre.light-theme .mb { color: #444444 !important} /* Literal.Number.Bin */
+pre.light-theme .mf { color: #444444 !important} /* Literal.Number.Float */
+pre.light-theme .mh { color: #444444 !important} /* Literal.Number.Hex */
+pre.light-theme .mi { color: #444444 !important} /* Literal.Number.Integer */
+pre.light-theme .mo { color: #444444 !important} /* Literal.Number.Oct */
+pre.light-theme .sa { color: #444444 !important} /* Literal.String.Affix */
+pre.light-theme .sb { color: #b83838 !important} /* Literal.String.Backtick */
+pre.light-theme .sc { color: #a848a8 !important} /* Literal.String.Char */
+pre.light-theme .dl { color: #b85820 !important} /* Literal.String.Delimiter */
+pre.light-theme .sd { color: #b85820; font-style: italic !important} /* Literal.String.Doc */
+pre.light-theme .s2 { color: #b83838 !important} /* Literal.String.Double */
+pre.light-theme .se { color: #709030 !important} /* Literal.String.Escape */
+pre.light-theme .sh { color: #b83838 !important} /* Literal.String.Heredoc */
+pre.light-theme .si { color: #b83838; text-decoration: underline !important} /* Literal.String.Interpol */
+pre.light-theme .sx { color: #a848a8 !important} /* Literal.String.Other */
+pre.light-theme .sr { color: #a848a8 !important} /* Literal.String.Regex */
+pre.light-theme .s1 { color: #b83838 !important} /* Literal.String.Single */
+pre.light-theme .ss { color: #b83838 !important} /* Literal.String.Symbol */
+pre.light-theme .bp { color: #388038; font-style: italic !important} /* Name.Builtin.Pseudo */
+pre.light-theme .fm { color: #b85820 !important} /* Name.Function.Magic */
+pre.light-theme .vc { color: #b04040 !important} /* Name.Variable.Class */
+pre.light-theme .vg { color: #908828 !important} /* Name.Variable.Global */
+pre.light-theme .vi { color: #b04040 !important} /* Name.Variable.Instance */
+pre.light-theme .vm { color: #b85820 !important} /* Name.Variable.Magic */
+pre.light-theme .il { color: #444444 !important} /* Literal.Number.Integer.Long */
+pre.light-theme .n { color: #444444 !important} /* Misc */
+pre.light-theme .o { color: #444 !important} /* Misc */
+pre.light-theme .p { color: #444 !important} /* Misc */
+pre.light-theme .k { color: #a848a8 !important} /* Misc */
+pre.light-theme .kc { color: #2838b0 !important} /* Misc */

docs/api_docs/tes.rst

@@ -0,0 +1,34 @@
+py-tes
+===========
+
+.. toctree::
+   :caption: API Docs
+   :name: api_docs
+   :hidden:
+   :maxdepth: 1
+
+   api_docs/tes
+
+tes.client module
+-----------------
+
+.. automodule:: tes.client
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tes.models module
+-----------------
+
+.. automodule:: tes.models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tes.utils module
+----------------
+
+.. automodule:: tes.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/conf.py

@@ -16,15 +16,13 @@
 import sys
 import os
 from sphinxawesome_theme.postprocess import Icons
-
+import tes
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath("../"))
 
-import tes
-
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -127,8 +125,8 @@
     "logo_light": "logo-ga4gh-light.png",
     "logo_dark": "logo-ga4gh-dark.png",
     "main_nav_links": {
-        "About": "index",
-        "API": "api/tes",
+        "About": "https://github.com/ohsu-comp-bio/py-tes",
+        "Docs": "https://github.com/ohsu-comp-bio/py-tes",
         "GitHub": "https://github.com/ohsu-comp-bio/py-tes",
     },
     "awesome_external_links": True,

docs/index.rst

@@ -6,13 +6,12 @@
 py-tes
 ======
 
-.. image:: https://img.shields.io/github/actions/workflow/status/ohsu-comp-bio/py-tes/tests.yml?logo=github
-   :alt: GitHub Actions Test Status
-   :target: https://github.com/ohsu-comp-bio/py-tes/actions
+.. image:: https://travis-ci.org/ohsu-comp-bio/py-tes.svg?branch=master
+    :target: https://travis-ci.org/ohsu-comp-bio/py-tes
 .. image:: https://coveralls.io/repos/github/ohsu-comp-bio/py-tes/badge.svg?branch=master
-   :target: https://coveralls.io/github/ohsu-comp-bio/py-tes?branch=master
+    :target: https://coveralls.io/github/ohsu-comp-bio/py-tes?branch=master
 .. image:: https://img.shields.io/badge/License-MIT-yellow.svg
-   :target: https://opensource.org/licenses/MIT
+    :target: https://opensource.org/licenses/MIT
 
 *py-tes* is a library for interacting with servers implementing the
 `GA4GH Task Execution
@@ -30,11 +29,10 @@ Available on `PyPI <https://pypi.org/project/py-tes/>`__.
 Example
 ~~~~~~~
 
-.. code:: python
+::
 
    import tes
 
-   # define task
    task = tes.Task(
        executors=[
            tes.Executor(
@@ -44,167 +42,36 @@ Example
        ]
    )
 
-   # create client
-   cli = tes.HTTPClient("https://funnel.example.com", timeout=5)
-
-   # access endpoints
-   service_info = cli.get_service_info()
+   cli = tes.HTTPClient("http://funnel.example.com", timeout=5)
    task_id = cli.create_task(task)
-   task_info = cli.get_task(task_id, view="BASIC")
+   res = cli.get_task(task_id)
    cli.cancel_task(task_id)
-   tasks_list = cli.list_tasks(view="MINIMAL")  # default view
-
-How to…
-~~~~~~~
-
-   Makes use of the objects above…
-
-…export a model to a dictionary
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. code:: python
-
-   task_dict = task.as_dict(drop_empty=False)
-
-``task_dict`` contents:
-
-.. code:: console
-
-   {'id': None, 'state': None, 'name': None, 'description': None, 'inputs': None, 'outputs': None, 'resources': None, 'executors': [{'image': 'alpine', 'command': ['echo', 'hello'], 'workdir': None, 'stdin': None, 'stdout': None, 'stderr': None, 'env': None}], 'volumes': None, 'tags': None, 'logs': None, 'creation_time': None}
-
-…export a model to JSON
-^^^^^^^^^^^^^^^^^^^^^^^
-
-.. code:: python
-
-   task_json = task.as_json()  # also accepts `drop_empty` arg
-
-``task_json`` contents:
-
-.. code:: console
-
-   {"executors": [{"image": "alpine", "command": ["echo", "hello"]}]}
-
-…pretty print a model
-^^^^^^^^^^^^^^^^^^^^^
-
-.. code:: python
-
-   print(task.as_json(indent=3))  # keyword args are passed to `json.dumps()`
-
-Output:
-
-.. code:: json
-
-   {
-      "executors": [
-         {
-            "image": "alpine",
-            "command": [
-               "echo",
-               "hello"
-            ]
-         }
-      ]
-   }
-
-…access a specific task from the task list
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. code:: python
-
-   specific_task = tasks_list.tasks[5]
 
-``specific_task`` contents:
-
-.. code:: console
-
-   Task(id='393K43', state='COMPLETE', name=None, description=None, inputs=None, outputs=None, resources=None, executors=None, volumes=None, tags=None, logs=None, creation_time=None)
-
-…iterate over task list items
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. code:: python
-
-   for t in tasks_list[:3]:
-       print(t.as_json(indent=3))
-
-Output:
-
-.. code:: console
-
-   {
-      "id": "task_A2GFS4",
-      "state": "RUNNING"
-   }
-   {
-      "id": "task_O8G1PZ",
-      "state": "CANCELED"
-   }
-   {
-      "id": "task_W246I6",
-      "state": "COMPLETE"
-   }
-
-…instantiate a model from a JSON representation
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. code:: python
-
-   task_from_json = tes.client.unmarshal(task_json, tes.Task)
-
-``task_from_json`` contents:
-
-.. code:: console
-
-   Task(id=None, state=None, name=None, description=None, inputs=None, outputs=None, resources=None, executors=[Executor(image='alpine', command=['echo', 'hello'], workdir=None, stdin=None, stdout=None, stderr=None, env=None)], volumes=None, tags=None, logs=None, creation_time=None)
-
-Which is equivalent to ``task``:
-
-.. code:: python
-
-   print(task_from_json == task)
-
-Output:
-
-.. code:: console
-
-   True
 
 .. _main-support:
 
+-------
 Support
-~~~~~~~
+-------
 
 * For releases, see :ref:`Changelog <changelog>`.
 * Check :ref:`frequently asked questions (FAQ) <project_info-faq>`.
 * For **bugs and feature requests**, please use the `issue tracker <https://github.com/ohsu-comp-bio/tes/issues>`_.
-* For **contributions**, visit py-tes on `Github <https://github.com/ohsu-comp-bio/py-tes>`_
+* For **contributions**, visit py-tes on `Github <https://github.com/ohsu-comp-bio/tes>`_ and read the :ref:`guidelines <project_info-contributing>`.
 
 .. _main-resources:
 
+---------
 Resources
-~~~~~~~~~
-
-`cwl-tes <https://github.com/ohsu-comp-bio/cwl-tes>`_
-    cwl-tes submits your tasks to a TES server. Task submission is parallelized when possible. 
-
-`Funnel <https://ohsu-comp-bio.github.io/funnel/>`_
-    Funnel is a toolkit for distributed task execution with a simple API.
-
-`ga4gh-tes <https://github.com/microsoft/ga4gh-tes>`_
-    C# implementation of the GA4GH TES API; provides distributed batch task execution on Microsoft Azure 
-
-`Nextflow <https://www.nextflow.io/>`_
-    Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. 
+---------
 
-`Snakemake <https://snakemake.github.io/>`_
-    The Snakemape workflow management system is a tool to create reproducible and scalable data analyses
+`Snakemake Wrappers Repository <https://snakemake-wrappers.readthedocs.org>`_
+    The Snakemake Wrapper Repository is a collection of reusable wrappers that allow to quickly use popular tools from Snakemake rules and workflows.
 
 .. toctree::
    :caption: API
-   :name: api
+   :name: api_docs
    :hidden:
    :maxdepth: 1
 
-   api/tes
+   api_docs/tes

docs/requirements.txt

@@ -9,6 +9,4 @@ immutables
 sphinxawesome-theme
 snakemake-interface-common
 snakemake-interface-executor-plugins
-snakemake-interface-storage-plugins
-attrs
-python-dateutil
+snakemake-interface-storage-plugins