Updates to more recent dependencies

.github/workflows/tests.yml

@@ -0,0 +1,34 @@
+name: Run Sumatra tests
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, macos-latest]
+        python-version: ["3.8", "3.9", "3.11", "3.12"]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r ci/requirements.txt
+          pip install -r ci/requirements-test.txt
+          pip install .
+          pip freeze
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          #flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings.
+          #flake8 . --count --exit-zero --max-complexity=10 --max-line-length=119 --statistics
+      - name: Test with pytest
+        run: |
+          pytest test/unittests

.gitignore

@@ -14,4 +14,7 @@ MANIFEST
 .pydevproject
 .komodoproject
 .idea
-*.egg-info
+*.egg-info
+env
+env-ci
+test/example_repositories/mercurial/hg/wcache

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2015 The Sumatra authors and contributors
+Copyright (c) 2025 The Sumatra authors and contributors
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

README.rst

@@ -26,61 +26,54 @@ For documentation, see http://packages.python.org/Sumatra/ and http://neuralense
 
 Functionality:
 
-    * launch simulations and analyses, and record various pieces of information,
-      including:
+* launch simulations and analyses, and record various pieces of information,
+  including:
 
-        - the executable (identity, version)
-        - the script (identity, version)
-        - the parameters
-        - the duration (execution time)
-        - console output
-        - links to all data (whether in files, in a database, etc.) produced by
-          the simulation/analysis
-        - the reason for doing the simulation/analysis
-        - the outcome of the simulation/analysis
+    - the executable (identity, version)
+    - the script (identity, version)
+    - the parameters
+    - the duration (execution time)
+    - console output
+    - links to all data (whether in files, in a database, etc.) produced by
+      the simulation/analysis
+    - the reason for doing the simulation/analysis
+    - the outcome of the simulation/analysis
 
-    * allow browsing/searching/visualising the results of previous experiments
-    * allow the re-running of previous simulations/analyses with automatic
-      verification that the results are unchanged
-    * launch single or batch experiments, serial or parallel
+* allow browsing/searching/visualising the results of previous experiments
+* allow the re-running of previous simulations/analyses with automatic
+  verification that the results are unchanged
+* launch single or batch experiments, serial or parallel
 
 
 ============
 Requirements
 ============
 
-Sumatra requires Python versions 2.7, 3.4, 3.5 or 3.6. The web interface requires
-Django (>= 1.8) and the django-tagging package.
+Sumatra requires Python version 3.4 or later The web interface requires
+Django (>= 2.2) and the django-tagging package.
 Sumatra requires that you keep your own code in a version control
 system (currently Subversion, Mercurial, Git and Bazaar are supported). If you
 are already using Bazaar there is nothing else to install. If you
-are using Subversion you will need to install the pysvn package. If you using
+are using Subversion you will need to install the pysvn package. If you are using
 Git, you will need to install git-python bindings, and for Mercurial install hg-api.
 
 
 ============
 Installation
 ============
 
-These instructions are for Unix, Mac OS X. They may work on Windows as well, but
+These instructions are for Unix and Mac OS. They may work on Windows as well, but
 it hasn't been thoroughly tested.
 
-If you have downloaded the source package, Sumatra-0.7.0.tar.gz::
-
-    $ tar xzf Sumatra-0.7.0.tar.gz
-    $ cd Sumatra-0.7.0
-    # python setup.py install
-
-The last step may have to be done as root.
-
-
-Alternatively, you can install directly from the Python Package Index::
+The easiest way to install is with pip::
 
     $ pip install sumatra
 
-or::
+Alternatively, you can download the source package, Sumatra-0.8.0.tar.gz from the Python Package Index::
 
-    $ easy_install sumatra
+    $ tar xzf Sumatra-0.8.0.tar.gz
+    $ cd Sumatra-0.8.0
+    $ python setup.py install
 
 You will also need to install Python bindings for the version control system(s) you use, e.g.::
 
@@ -92,8 +85,8 @@ You will also need to install Python bindings for the version control system(s)
 Code status
 ===========
 
-.. image:: https://travis-ci.org/open-research/sumatra.png?branch=master
-   :target: https://travis-ci.org/open-research/sumatra
+.. image:: https://github.com/open-research/sumatra/actions/workflows/tests/badge.svg
+   :target: https://github.com/open-research/sumatra/actions/workflows/tests.yml
    :alt: Unit Test Status
 
 .. image:: https://coveralls.io/repos/open-research/sumatra/badge.svg

bin/smtweb

@@ -68,8 +68,16 @@ def main(argv):
         INSTALLED_APPS=db_config._settings["INSTALLED_APPS"] + ['sumatra.web'],
         ROOT_URLCONF='sumatra.web.urls',
         STATIC_URL='/static/',
-        TEMPLATE_DIRS=(os.path.join(os.getcwd(), ".smt", "templates"),
-                       os.path.join(root_dir, "templates"),),
+        TEMPLATES=[
+            {
+                'BACKEND': 'django.template.backends.django.DjangoTemplates',
+                'APP_DIRS': False,
+                'DIRS': [
+                    os.path.join(os.getcwd(), ".smt", "templates"),
+                    os.path.join(root_dir, "templates")
+                ]
+            },
+        ],
         MIDDLEWARE_CLASSES=tuple(),
         READ_ONLY = options.read_only,
         SERVERSIDE = options.serverside,

ci/requirements-test.txt

@@ -3,7 +3,7 @@ sarge
 numpy
 scipy
 matplotlib
-nose
 pillow
-coverage
-coveralls
+pytest<8
+pytest-cov
+flake8

ci/requirements.txt

@@ -1,12 +1,13 @@
 # Base requirements for running Sumatra, for all supported versions of Python
-Django>=1.8
+setuptools  # needed for Python 3.12, since distutils removed
+Django<3
 django-tagging>=0.4
 httplib2
 jinja2
 docutils
 parameters
-future
 # optional requirements, depending on which version control systems you use
+mercurial
 hgapi
 GitPython>=0.3.6
 # optional requirements, depending on which serialization formats you want
@@ -15,4 +16,4 @@ pyyaml
 #dexml
 #fs
 # optional, for PostgreSQL support
-#psycopg2
+#psycopg2

doc/build_reference.py

@@ -1,6 +1,3 @@
-from __future__ import unicode_literals
-from future import standard_library
-standard_library.install_aliases()
 import sys
 from sumatra import commands
 from io import StringIO
@@ -24,16 +21,15 @@
 
 sys.stdout = sys.__stdout__
 
-f = open("command_reference.txt", "w")
-f.write("=====================\n")
-f.write("smt command reference\n")
-f.write("=====================\n\n")
-
-for mode in modes:
-    sio = usage[mode]
-    f.write(mode + '\n')
-    f.write('-'*len(mode) + '\n::\n\n    ')
-    sio.seek(0)
-    f.write("    ".join(sio.readlines()) + '\n')
-    sio.close()
-f.close()
+with open("command_reference.txt", "w") as f:
+    f.write("=====================\n")
+    f.write("smt command reference\n")
+    f.write("=====================\n\n")
+
+    for mode in modes:
+        sio = usage[mode]
+        f.write(mode + '\n')
+        f.write('-'*len(mode) + '\n::\n\n    ')
+        sio.seek(0)
+        f.write("    ".join(sio.readlines()) + '\n')
+        sio.close()

doc/conf.py

@@ -11,7 +11,6 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-from __future__ import unicode_literals
 import sys, os
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -40,7 +39,7 @@
 # General information about the project.
 project = 'Sumatra'
 authors = 'Sumatra authors and contributors'
-copyright = '2009-2015 ' + authors
+copyright = '2009-2020, 2024-2025 ' + authors
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the