Merge pull request #9 from molssi-seamm/dev

Moved Jobs from threads to independent processes.

.github/workflows/CI.yaml

@@ -7,11 +7,6 @@ on:
   pull_request:
     branches:
       - "main"
-  schedule:
-    # Run on master by default Sunday morning at 3:30:
-    #   Scheduled workflows run on the latest commit on the default or base branch.
-    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
-    - cron: "30 3 * * 0"
 
 jobs:
   ci:

.github/workflows/CodeQL.yaml

@@ -0,0 +1,13 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main" ]
+
+jobs:
+  codeql:
+    name: CodeQL
+    uses: molssi-seamm/devops/.github/workflows/CodeQL.yaml@main

.gitignore

@@ -147,6 +147,3 @@ target/
 # Cookiecutter
 output/
 python_boilerplate/
-
-# pyenv python configuration file
-.python-version

HISTORY.rst

@@ -2,6 +2,13 @@
 History
 =======
 
+2023.3.23 -- Substantial improvements to JobServer
+   * Switched to independent process for Jobs, which means they are fully independent of
+     the JobServer and continue to run if the JobServer stops
+   * Discover existing running jobs on startup and monitor them.
+   * Added status information for the machine the JobServer is on as well as Jobs
+   * Provide a GUI if run from the commandline, showing the log and status.
+
 0.9.1 (2020-05-29)
 ------------------
 

Makefile

@@ -1,6 +1,9 @@
 MODULE := seamm_jobserver
-.PHONY: clean clean-test clean-pyc clean-build docs help
+.PHONY: help clean clean-build clean-docs clean-pyc clean-test lint format typing test
+.PHONY: dependencies test-all coverage html docs servedocs release check-release
+.PHONY: dist install uninstall
 .DEFAULT_GOAL := help
+
 define BROWSER_PYSCRIPT
 import os, webbrowser, sys
 try:
@@ -10,6 +13,7 @@ except:
 
 webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
 endef
+
 export BROWSER_PYSCRIPT
 
 define PRINT_HELP_PYSCRIPT
@@ -21,7 +25,9 @@ for line in sys.stdin:
 		target, help = match.groups()
 		print("%-20s %s" % (target, help))
 endef
+
 export PRINT_HELP_PYSCRIPT
+
 BROWSER := python -c "$$BROWSER_PYSCRIPT"
 
 help:
@@ -47,32 +53,37 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .tox/
 	rm -f .coverage
 	rm -fr htmlcov/
+	find . -name '.pytype' -exec rm -fr {} +
 
-lint: ## check style with yapf
-	black --check --diff --extend-exclude '_version.py' $(MODULE) tests
-	flake8 $(MODULE) tests
+lint: ## check style with black and flake8
+	black --extend-exclude '_version.py' --check --diff $(MODULE) tests
+	flake8 --color never $(MODULE) tests
 
 format: ## reformat with with yapf and isort
 	black --extend-exclude '_version.py' $(MODULE) tests
 
 test: ## run tests quickly with the default Python
-	py.test
-
-test-all: ## run tests on every Python version with tox
-	tox
+	pytest tests/
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source $(MODULE) -m pytest
-	coverage report -m
-	coverage html
+	pytest -v --cov=$(MODULE) --cov-report term --color=yes tests/
+
+coverage-html: ## check code coverage quickly with the default Python, showing as html
+	pytest -v --cov=$(MODULE) --cov-report=html:htmlcov --cov-report term --color=yes tests/
 	$(BROWSER) htmlcov/index.html
 
-docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/$(MODULE).rst
-	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ $(MODULE)
+clean-docs: ## remove files associated with building the docs
+	rm -f docs/api/$(MODULE).rst
+	rm -f docs/api/modules.rst
 	$(MAKE) -C docs clean
+
+html: clean-docs ## generate Sphinx HTML documentation, including API docs
+	sphinx-apidoc -o docs/api $(MODULE)
 	$(MAKE) -C docs html
+	rm -f docs/api/$(MODULE).rst
+	rm -f docs/api/modules.rst
+
+docs: html ## Make the html docs and show in the browser
 	$(BROWSER) docs/_build/html/index.html
 
 servedocs: docs ## compile the docs watching for changes
@@ -93,4 +104,3 @@ install: uninstall ## install the package to the active Python's site-packages
 
 uninstall: clean ## uninstall the package
 	pip uninstall --yes $(MODULE)
-

README.rst

@@ -3,54 +3,56 @@ SEAMM JobServer
 ===============
 
 
-.. image:: https://img.shields.io/travis/molssi-seamm/seamm_jobserver.svg
-           :target: https://travis-ci.org/molssi-seamm/seamm_jobserver
-	   :alt: Build Status
+.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/seamm_jobserver
+   :target: https://github.com/molssi-seamm/seamm_jobserver/pulls
+   :alt: GitHub pull requests
 
-.. image:: https://codecov.io/gh/molssi-seamm/seamm_jobserver/branch/master/graph/badge.svg
-	   :target: https://codecov.io/gh/molssi-seamm/seamm_jobserver
-	   :alt: Code Coverage
+.. image:: https://github.com/molssi-seamm/seamm_jobserver/workflows/CI/badge.svg
+   :target: https://github.com/molssi-seamm/seamm_jobserver/actions
+   :alt: Build Status
 
-.. image:: https://img.shields.io/lgtm/grade/python/g/molssi-seamm/seamm_jobserver.svg?logo=lgtm&logoWidth=18
-	   :target: https://lgtm.com/projects/g/molssi-seamm/seamm_jobserver/context:python
-	   :alt: Code Quality
+.. image:: https://codecov.io/gh/molssi-seamm/seamm_jobserver/branch/main/graph/badge.svg
+   :target: https://codecov.io/gh/molssi-seamm/seamm_jobserver
+   :alt: Code Coverage
 
-.. image:: https://readthedocs.org/projects/mopac-step/badge/?version=latest
-           :target: https://mopac-step.readthedocs.io/en/latest/?badge=latest
-	   :alt: Documentation Status
+.. image:: https://github.com/molssi-seamm/seamm_jobserver/workflows/CodeQL/badge.svg
+   :target: https://github.com/molssi-seamm/seamm_jobserver/security/code-scanning
+   :alt: Code Quality
 
-.. image:: https://pyup.io/repos/github/molssi-seamm/seamm_jobserver/shield.svg
-	   :target: https://pyup.io/repos/github/molssi-seamm/seamm_jobserver/
-	   :alt: Updates for Dependencies
+.. image:: https://github.com/molssi-seamm/seamm_jobserver/workflows/Release/badge.svg
+   :target: https://molssi-seamm.github.io/seamm_jobserver/index.html
+   :alt: Documentation Status
 
 .. image:: https://img.shields.io/pypi/v/seamm_jobserver.svg
-           :target: https://pypi.python.org/pypi/seamm_jobserver
-	   :alt: PyPi VERSION
+   :target: https://pypi.python.org/pypi/seamm_jobserver
+   :alt: PyPi VERSION
 
 
 The JobServer for the SEAMM environment
 
 
 * Free software: BSD license
-* Documentation: https://seamm-jobserver.readthedocs.io.
+* Documentation: https://molssi-seamm.github.io/seamm_jobserver/index.html
+* Code: https://github.com/molssi-seamm/seamm_jobserver
 
 
 Features
 --------
 
-* TODO
+The SEAMM JobServer handles executing Jobs for the Dashboard.
 
-Credits
--------
 
-This package was created with Cookiecutter_ and the `molssi-seamm/cookiecutter-seamm-plugin`_ project template.
+Acknowledgements
+----------------
+
+This package was created with the `molssi-seamm/cookiecutter-seamm-plugin`_ tool, which
+is based on the excellent Cookiecutter_.
 
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin
 
-Developed by the Molecular Sciences Software Institute (MolSSI_),
-which receives funding from the `National Science Foundation`_ under
-award OAC-1547580 and CHE-2136142.
+Developed by the Molecular Sciences Software Institute (MolSSI_), which receives funding
+from the `National Science Foundation`_ under award CHE-2136142.
 
-.. _MolSSI: https://www.molssi.org
+.. _MolSSI: https://molssi.org
 .. _`National Science Foundation`: https://www.nsf.gov

devtools/conda-envs/test_env.yaml

@@ -10,6 +10,7 @@ dependencies:
 
   # Dependencies for this module
   - seamm
+  - psutil
 
   # Testing
   - black
@@ -18,16 +19,12 @@ dependencies:
   - pytest
   - pytest-cov
 
-  - py-cpuinfo
+  # Documentation
+  - pydata-sphinx-theme
+  - sphinx-design
 
   # Pip-only installs
   - pip:
-    # Testing
-    - yapf
-
     # Documentation
-    - rinohtype
-    - pygments
-    - sphinx-rtd-theme
-    - pystemmer
-
+    - sphinx-copybutton
+    - sphinxnotes-strike

docs/_static/README.md

@@ -0,0 +1,16 @@
+# Static Doc Directory
+
+Add any paths that contain custom static files (such as style sheets) here,
+relative to the `conf.py` file's directory. 
+They are copied after the builtin static files,
+so a file named "default.css" will overwrite the builtin "default.css".
+
+The path to this folder is set in the Sphinx `conf.py` file in the line: 
+```python
+templates_path = ['_static']
+```
+
+## Examples of file to add to this directory
+* Custom Cascading Style Sheets
+* Custom JavaScript code
+* Static logo images

docs/_static/css/custom.css

@@ -0,0 +1,73 @@
+@import "../basic.css";
+
+html[data-theme="light"] {
+    --pst-color-primary: #ed1c24;
+	--pst-color-warning: #ed1c24;
+	--pst-color-primary-highlight: #bc151b;
+	--pst-color-secondary: #1d35e7;
+	--pst-color-secondary-highlight: #3e51e3;
+
+}
+
+html[data-theme="dark"] {
+    --pst-color-primary: #ed1c24;
+	--pst-color-warning: #ed1c24;
+	--pst-color-primary-highlight: #bc151b;
+	--pst-color-background: #1A1A1A;
+	--pst-color-secondary: #1d35e7;
+	--pst-color-secondary-highlight: #3e51e3;
+
+
+}
+
+html[data-theme="light"] a:hover {
+	color: #1A1A1A;
+}
+
+html[data-theme="dark"] h1, html[data-theme="dark"] h2, html[data-theme="dark"] h3, html[data-theme="dark"] h4, html[data-theme="dark"] h5, html[data-theme="dark"] h6 {
+	color: #ffffff;
+}
+
+
+html[data-theme="dark"] a {
+	color: #ffffff;
+}
+
+html[data-theme="dark"] .reference.external {
+	text-decoration: underline;
+
+}
+
+html[data-theme="dark"] p .reference.internal {
+	text-decoration: underline;
+
+}
+
+html[data-theme="dark"] a:hover {
+	color: #ed1c24;
+}
+
+html[data-theme="dark"] .prev-next-area a p.prev-next-title {
+    color: white;
+}
+
+html[data-theme="dark"] .prev-next-area:hover a:hover p.prev-next-title:hover {
+    color: #ed1c24;
+}
+
+html[data-theme="dark"] dt:target {
+    background-color: #000000;
+}
+
+html .toctree-wrapper li[class^=toctree-l] {
+	list-style: circle;
+}
+
+img:not(.logo__image, .footer_logo) {
+	padding: 20px;
+}
+
+
+.footer_logo {
+	max-height: 60px;
+}

docs/_templates/README.md

@@ -0,0 +1,14 @@
+# Templates Doc Directory
+
+Add any paths that contain templates here, relative to  
+the `conf.py` file's directory.
+They are copied after the builtin template files,
+so a file named "page.html" will overwrite the builtin "page.html".
+
+The path to this folder is set in the Sphinx `conf.py` file in the line: 
+```python
+html_static_path = ['_templates']
+```
+
+## Examples of file to add to this directory
+* HTML extensions of stock pages like `page.html` or `layout.html`