Devel (#171)

* Minor bug fixes surrounding visualization due to matplotlib 3.3 deprecations temp fix for NLEQ2 bug, use newton_linesearch instead bumpversion Documentation updates and fixes bug fix in OptGp sampler set commit to True Bump version: 0.1.6rc0 → 0.1.6 * Turn off notebook execution (too long to run each time) * pre-commit autoupdate adjusted repostory link for flake8 Removed .bumpversion.cfg from manifest, now merged with setup.cfg Removed safety from tox testing workflow Unicode string prefix removed setup.cfg updates for README and deprecations in setuptools URL updates Changed to assert statement due to return True deprecation intersphinx link updates Removed 3.10 until further testing * Updates to test workflow file Relaxed versioning requirements Late add of 0.1.6 release notes Dropped Python 3.6 support and updated files for deprecation warnings broken link fixes Escher conflict with versioning jinja2<3 but requirements are for jinja2>3, temp workaround for now with explicit ipywidget inclusion * Temp solution to address sys-bio/roadrunner#651 * retry * try linking ncurses with softlink * Try using older ubuntu image * Try updating libc6 for py39 dependency and replace ubuntu-latest with ubuntu-20.04 until ncurses issue addressed in libroadrunner * revert back to latest * Removed empty cell at top of notebook Updated pandas append to concat to fix deprecation tutorial update Update roadrunner to v2.2 * Bump version: 0.1.7rc0 → 0.1.7
SBRG · Dec 9, 2022 · 784bda5 · 784bda5
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -20,10 +20,10 @@ on:
         pip_opts:
           description: Install options (pip)
           required: false
-          default: '--upgrade --upgrade-strategy eager'
+          default: '--upgrade'
 env:
   ACTIONS_SETUP_PY3: ${{ github.event.inputs.py-act || '3.9' }}
-  PIP_INSTALL_OPTS: ${{ github.event.inputs.pip_opts || '--upgrade --upgrade-strategy eager' }}
+  PIP_INSTALL_OPTS: ${{ github.event.inputs.pip_opts || '--upgrade' }}
   PY_COLORS: 1
   DOCKER_IMAGE: sbrg/masspy
 
@@ -57,7 +57,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        py: [3.6, 3.7, 3.8, 3.9]
+        py: [3.7, 3.8, 3.9]
     steps:
       -
         name: Checkout repository

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@ default_language_version:
     python: python3
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.0.1
+      rev: v4.4.0
       hooks:
       - id: check-merge-conflict
       - id: check-toml
@@ -33,10 +33,10 @@ repos:
       hooks:
       - id: isort
     - repo: https://github.com/psf/black
-      rev: 21.12b0
+      rev: 22.10.0
       hooks:
       - id: black
-    - repo: https://gitlab.com/pycqa/flake8
-      rev: 3.9.2
+    - repo: https://github.com/pycqa/flake8
+      rev: 6.0.0
       hooks:
       - id: flake8
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,7 +1,6 @@
 include \
     *.yml \
     *.yaml \
-    .bumpversion.cfg \
     .dockerignore
 
 graft docker

diff --git a/README.md b/README.md
@@ -30,7 +30,7 @@ workflows and techniques. Additional information about [**COBRApy**][11] can be
 
 Check out the following information from the [Quick Start](https://masspy.readthedocs.io/en/latest/installation/quickstart.html) guide to get started using MASSpy!
 
-### With Python 3.6+
+### With Python 3.7+
 
 The recommended method is to install **MASSpy** is to use ``pip`` to
 install the software from the [Python Package Index](https://pypi.org/project/masspy/)

diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -1,5 +1,5 @@
 ARG python_version=3.7
-ARG mass_version=0.1.7rc0
+ARG mass_version=0.1.7
 # Image to checkout and install a specific version of MASSpy
 FROM python:${python_version} AS env-setup
 ARG python_version

diff --git a/docs/additional/code_repositories.rst b/docs/additional/code_repositories.rst
@@ -46,6 +46,6 @@ As a helpful reference, links to the documentation homepages are provided for a
 * `Matplotlib <https://matplotlib.org/>`__
 * `pandas <https://pandas.pydata.org/>`__
 * `SymPy <https://www.sympy.org/>`__
-* `libRoadRunner <http://libroadrunner.org/>`__
-* `iPython <http://ipython.org/>`__ (`Jupyter <https://jupyter.org/>`__)
+* `libRoadRunner <https://www.libroadrunner.org/>`__
+* `iPython <https://ipython.org/>`__ (`Jupyter <https://jupyter.org/>`__)
 * `Docker <https://docs.docker.com/>`__
diff --git a/docs/conf.py b/docs/conf.py
@@ -121,13 +121,13 @@
 
 # Refer to the Python documentation for other libraries.
 intersphinx_mapping = {
-    "http://docs.python.org/": None,
+    "https://docs.python.org/3/": None,
     "https://cobrapy.readthedocs.io/en/latest/": None,
     "https://libroadrunner.readthedocs.io/en/latest/": None,
     "https://matplotlib.org/stable/": None,
-    "http://docs.scipy.org/doc/numpy/": None,
+    "https://numpy.org/doc/stable/": None,
     "https://pandas.pydata.org/pandas-docs/stable/": None,
-    "http://docs.scipy.org/doc/scipy/reference": None,
+    "https://docs.scipy.org/doc/scipy/": None,
     "https://docs.sympy.org/latest": None,
 }
 intersphinx_cache_limit = 10  # days to keep the cached inventories
diff --git a/docs/education/sb2/chapters/sb2_chapter13.ipynb b/docs/education/sb2/chapters/sb2_chapter13.ipynb
diff --git a/docs/education/sb2/chapters/sb2_chapter14.ipynb b/docs/education/sb2/chapters/sb2_chapter14.ipynb
diff --git a/docs/education/sb2/chapters/sb2_chapter8.ipynb b/docs/education/sb2/chapters/sb2_chapter8.ipynb
@@ -2813,7 +2813,9 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "\u001b[93mWARNING:\u001b[0m \u001b[93mNo compartments found in model. Therefore creating compartment 'compartment' for entire model.\u001b[0m\n"
+      "\u001b[93mWARNING:\u001b[0m \u001b[93mNo compartments found in model. Therefore creating compartment 'compartment' for entire model.\u001b[0m\n",
+      "\u001b[93mWARNING:\u001b[0m \u001b[93mNo compartments found in model. Therefore creating compartment 'compartment' for entire model.\u001b[0m\n",
+      "\u001b[91mERROR:\u001b[0m \u001b[91mSomething unexpected occurred and the model could not be loaded into the current RoadRunner instance. Therefore initializing a new RoadRunner instance for the Simulation.\u001b[0m\n"
      ]
     },
     {

diff --git a/docs/gallery/visualization/animating_simulations.ipynb b/docs/gallery/visualization/animating_simulations.ipynb
diff --git a/docs/installation/solvers.rst b/docs/installation/solvers.rst
@@ -35,7 +35,7 @@ The *Gurobi Optimizer* (Gurobi) is utilized through the `Gurobi Python Interface
 * To use Gurobi, a license must be obtained. Free academic licences are available.
 * To use Gurobi with Docker, a floating license is required.
 
-  `Homepage <https://www.gurobi.com/products/gurobi-optimizer/>`__ |
+  `Homepage <hhttps://www.gurobi.com/solutions/gurobi-optimizer/>`__ |
   `Documentation <https://www.gurobi.com/documentation/>`__ |
   `Academic License <https://www.gurobi.com/academia/academic-program-and-licenses/>`__ |
   `Floating License <https://www.gurobi.com/documentation/9.0/quickstart_linux/retrieving_a_floating_lice.html>`__

diff --git a/docs/tutorials/compartments.ipynb b/docs/tutorials/compartments.ipynb
@@ -332,8 +332,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "volume_l\n",
-      "volume_m\n"
+      "volume_m\n",
+      "volume_l\n"
      ]
     }
    ],

diff --git a/docs/tutorials/constructing_models.ipynb b/docs/tutorials/constructing_models.ipynb
@@ -1616,7 +1616,7 @@
    "metadata": {},
    "source": [
     "### Units\n",
-    "`Unit` and `UnitDefinition` objects are implemented as per the [SBML Unit](http://sbml.org/Software/libSBML/5.18.0/docs/python-api/classlibsbml_1_1_unit.html) and [SBML UnitDefinition](http://sbml.org/Software/libSBML/5.18.0/docs/python-api/classlibsbml_1_1_unit_definition.html) specifications.\n",
+    "`Unit` and `UnitDefinition` objects are implemented as per the [SBML Unit](https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/classlibsbml_1_1_unit.html) and [SBML UnitDefinition](https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/classlibsbml_1_1_unit_definition.html) specifications.\n",
     "It can be useful for comparative reasons to create `Unit` and `UnitDefinition` objects for the model (e.g., amount, volume, time) to provide additional context. However, the model does not maintain unit consistency automatically. It is the responsibility of the users to ensure consistency among units and associated numerical values in a model."
    ]
   },

diff --git a/docs/tutorials/dynamic_simulation.ipynb b/docs/tutorials/dynamic_simulation.ipynb
diff --git a/docs/tutorials/getting_started_with_masspy.ipynb b/docs/tutorials/getting_started_with_masspy.ipynb
@@ -317,7 +317,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "To ensure all identifiers comply with [Systems Biology Markup Language (SBML)](http://sbml.org/Main_Page) and allow for interactive use, utilizing the identifiers from the [BiGG Models database](http://bigg.ucsd.edu/) is highly recommended.\n",
+    "To ensure all identifiers comply with [Systems Biology Markup Language (SBML)](https://sbml.org/) and allow for interactive use, utilizing the identifiers from the [BiGG Models database](http://bigg.ucsd.edu/) is highly recommended.\n",
     "\n",
     "Guidelines for BiGG identifiers are found [here](https://github.com/SBRG/bigg_models/wiki/BiGG-Models-ID-Specification-and-Guidelines)."
    ]
@@ -1418,7 +1418,7 @@
    "metadata": {},
    "source": [
     "### Groups\n",
-    "Groups are objects for holding information regarding pathways, subsystems, or any custom grouping of objects within a `MassModel`. **MASSpy** directly utilizes the `cobra.Group` object, which are implemented based on the [SBML Group](http://sbml.org/Software/libSBML/5.18.0/docs/python-api/classlibsbml_1_1_group.html) specifications.\n",
+    "Groups are objects for holding information regarding pathways, subsystems, or any custom grouping of objects within a `MassModel`. **MASSpy** directly utilizes the `cobra.Group` object, which are implemented based on the [SBML Group](https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/group__groups.html) specifications.\n",
     "\n",
     "`Group` objects are stored in a `cobra.DictList` as the `groups` attribute of the `MassModel`."
    ]
@@ -1565,7 +1565,7 @@
    "source": [
     "### Units\n",
     "\n",
-    "`Unit` and `UnitDefinition` objects are implemented, as per the [SBML Unit](http://sbml.org/Software/libSBML/5.18.0/docs/python-api/classlibsbml_1_1_unit.html) and [SBML UnitDefinition](http://sbml.org/Software/libSBML/5.18.0/docs/python-api/classlibsbml_1_1_unit_definition.html) specifications. The primary purpose of these objects is to inform users of the model's units, providing context to model values and observed results.\n",
+    "`Unit` and `UnitDefinition` objects are implemented, as per the [SBML Unit](https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/classlibsbml_1_1_unit.html) and [SBML UnitDefinition](https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/classlibsbml_1_1_unit_definition.html) specifications. The primary purpose of these objects is to inform users of the model's units, providing context to model values and observed results.\n",
     "\n",
     "It is important to note that unit consistency is **NOT** checked by the `MassModel`, meaning that it is incumbent upon users to maintain consistency of units and associated numerical values in a model. \n",
     "\n",
@@ -1658,8 +1658,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "kind: mole; exponent: 1; scale: -3; multiplier: 1\n",
-      "kind: litre; exponent: -1; scale: 0; multiplier: 1\n"
+      "kind: litre; exponent: -1; scale: 0; multiplier: 1\n",
+      "kind: mole; exponent: 1; scale: -3; multiplier: 1\n"
      ]
     }
    ],
@@ -1723,7 +1723,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3.9.5 ('beng123')",
    "language": "python",
    "name": "python3"
   },
@@ -1737,7 +1737,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.15"
+   "version": "3.9.5"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "8e44e5c2ac5fdd4cabb24e42b49ad4e0bc098b81974ee0e625739ea45ccb12a4"
+   }
   }
  },
  "nbformat": 4,

diff --git a/docs/tutorials/network_visualization.ipynb b/docs/tutorials/network_visualization.ipynb
@@ -11,7 +11,7 @@
     "The **Escher** package must already be installed into the environment. To install **Escher**:\n",
     "\n",
     "```python\n",
-    "pip install escher\n",
+    "pip install escher>=1.7\n",
     "```\n",
     "\n",
     "## Viewing Models with Escher\n",
@@ -475,6 +475,17 @@
     "\n",
     "* [Animating Simulations with Escher](../gallery/visualization/animating_simulations.ipynb)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<div class=\"alert alert-warning\"> \n",
+    "Due to versioning compatibility issues, it is possible that Jinja2==3.1.2 must be installed. See issue \n",
+    "\n",
+    "* https://github.com/zakandrewking/escher/issues/377\n",
+    "</div>"
+   ]
   }
  ],
  "metadata": {

diff --git a/docs/tutorials/reading_writing_models.ipynb b/docs/tutorials/reading_writing_models.ipynb
@@ -166,7 +166,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "**MASSpy** utilizes the [libSBML](http://sbml.org/Software/libSBML/5.18.0/docs/python-api/) package to read and write SBML files, supporting both the [FBC](http://sbml.org/Software/libSBML/5.18.0/docs/python-api/group__fbc.html) (Version 2) and the [Groups](http://sbml.org/Software/libSBML/5.18.0/docs/python-api/group__groups.html) (Version 1) extensions.\n",
+    "**MASSpy** utilizes the [libSBML](https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/) package to read and write SBML files, supporting both the [FBC](https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/group__fbc.html (Version 2) and the [Groups](https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/group__groups.html) (Version 1) extensions.\n",
     "When reading in a model, **MASSpy** automatically detects whether the FBC and/or Groups extensions were used.\n",
     "\n",
     "To preserve information specific to `EnzymeModule` objects, the SBML Groups extension is used along with the notes section for SBML objects. The `use_groups_package` argument can be utilized to indicate whether to write `cobra.Group` objects to the SBML file, including `EnzymeModule` information. Disabling this extension may result in a loss of some enzyme specific information (e.g., categorized groups), but it does not prevent species and reactions of the enzyme module\n",
@@ -341,7 +341,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3.9.5 ('beng123')",
    "language": "python",
    "name": "python3"
   },
@@ -355,7 +355,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.15"
+   "version": "3.9.5"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "8e44e5c2ac5fdd4cabb24e42b49ad4e0bc098b81974ee0e625739ea45ccb12a4"
+   }
   }
  },
  "nbformat": 4,

diff --git a/docs/tutorials/thermo_concentrations.ipynb b/docs/tutorials/thermo_concentrations.ipynb
diff --git a/pyproject.toml b/pyproject.toml
@@ -15,7 +15,6 @@ build-backend = "setuptools.build_meta"
 [tool.black]
 line-length = 88
 python-version = [
-    "py36",
     "py37",
     "py38",
     "py39"
@@ -91,8 +90,7 @@ envlist =
     clean,
     lint,
     pypi-description,
-    safety,
-    py3{6,7,8,9},
+    py3{7,8,9},
     docs,
     report
 isolated_build = true
@@ -101,7 +99,6 @@ skip_missing_interpreters = true
 
 [gh-actions]
 python =
-    3.6: py36
     3.7: py37
     3.8: py38
     3.9: py39
@@ -116,10 +113,10 @@ setenv =
     PYTHONUNBUFFERED=yes
     PY_COLORS={env:PY_COLORS:1}
 usedevelop = true
-install_command = python -m pip install --upgrade --upgrade-strategy eager {opts} {packages}
+install_command = python -m pip install --upgrade {opts} {packages}
 depends =
-    py3{6,7,8,9}: clean
-    report: py3{6,7,8,9}
+    py3{7,8,9}: clean
+    report: py3{7,8,9}
 
 
 [testenv:clean]
@@ -140,6 +137,7 @@ setenv =
 deps =
     pre-commit
 commands =
+
     pre-commit install
     pre-commit autoupdate
     pre-commit run --all-files --show-diff-on-failure
@@ -154,7 +152,7 @@ commands =
     safety check --full-report
 
 
-[testenv:py3{6,7,8,9}]
+[testenv:py3{7,8,9}]
 description = Run tests under {basepython}.
 extras = tests
 commands =

diff --git a/release-notes/0.1.6.md b/release-notes/0.1.6.md
@@ -0,0 +1,3 @@
+# Release notes for MASSpy 0.1.6
+
+* This will be the last version of MASSpy to support Python 3.6.
diff --git a/release-notes/0.1.7.md b/release-notes/0.1.7.md
@@ -0,0 +1,9 @@
+# Release notes for MASSpy 0.1.7
+
+* Dropped support Python 3.6.
+
+## Fixes
+
+* Fixed versioning issues in installation
+* Fixed documentation issues
+* Other minor fixes
diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.7rc0
+current_version = 0.1.7
 commit = True
 tag = False
 tag_name = v{new_version}
@@ -51,17 +51,15 @@ classifiers =
 	Natural Language :: English
 	Operating System :: OS Independent
 	Programming Language :: Python :: 3
-	Programming Language :: Python :: 3.6
 	Programming Language :: Python :: 3.7
 	Programming Language :: Python :: 3.8
 	Programming Language :: Python :: 3.9
-	Programming Language :: Python :: 3.10
 	Topic :: Scientific/Engineering :: Bio-Informatics
 license = MIT
-license_file = LICENSE
+license_files = LICENSE
 description = MASSpy is a package for dynamic modeling of biological processes.
-long_description = file: README.rst
-long_description_content_type = text/x-rst
+long_description = file: README.md
+long_description_content_type = text/markdown
 keywords = 
 	python
 	metabolism
@@ -80,25 +78,23 @@ keywords =
 zip_safe = True
 install_requires = 
 	cobra<0.24.0
-	libroadrunner==2.1.3
-	numpy<1.22
+	libroadrunner~=2.2
+	numpy
 	scipy
 	optlang
 	pandas
 	scipy
 	six
 	sympy
 	tabulate
-python_requires = ~=3.6
-include_package_data = True
-packages = find:
+python_requires = ~=3.7
+packages = find_namespace:
 package_dir = 
 	= src
+include_package_data = True
 
 [options.packages.find]
 where = src
-include = 
-	mass
 
 [options.extras_require]
 visualization = 
@@ -109,7 +105,7 @@ development =
 	towncrier
 	tox
 docs = 
-	escher
+	ipywidgets
 	ipykernel
 	nbsphinx
 	notebook