Merge pull request #6 from gboeing/release

gboeing · web-flow · commit 2d8161a34dc9 · 2022-05-23T16:35:39.000-07:00
update for release v0.3.2
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.6', '3.7', '3.8', '3.9']
+        python-version: ['3.8', '3.9', '3.10']
 
     defaults:
       run:
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Change log
 
+## 0.3.2 (2022-05-23)
+
+  - update dependencies compatibility
+
 ## 0.3.1 (2021-01-01)
 
   - include requirements in distribution
@@ -31,4 +35,4 @@
 
 ## 0.1 (2016-12-27)
 
-  - first release
+  - first release
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2015-2021 Geoff Boeing https://geoffboeing.com/
+Copyright (c) 2015-2022 Geoff Boeing https://geoffboeing.com/
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/docker/requirements.txt b/docker/requirements.txt
@@ -17,5 +17,5 @@ pip
 pydocstyle
 pynamical
 pytest
-python == 3.8.*
+python == 3.10.*
 sphinx
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -61,13 +61,13 @@
 
 # General information about the project.
 project = "pynamical"
-copyright = "2015-2021, Geoff Boeing"
+copyright = "2015-2022, Geoff Boeing"
 author = "Geoff Boeing"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
-version = release = "0.3.1"
+version = release = "0.3.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/examples/pynamical-demo-3d-animation.ipynb b/examples/pynamical-demo-3d-animation.ipynb
@@ -450,7 +450,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,
diff --git a/examples/pynamical-demo-cobweb-plots.ipynb b/examples/pynamical-demo-cobweb-plots.ipynb
@@ -233,7 +233,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,
diff --git a/examples/pynamical-demo-logistic-model.ipynb b/examples/pynamical-demo-logistic-model.ipynb
@@ -295,7 +295,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,
diff --git a/examples/pynamical-demo-other-models.ipynb b/examples/pynamical-demo-other-models.ipynb
@@ -214,7 +214,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,
diff --git a/examples/pynamical-demo-phase-diagrams.ipynb b/examples/pynamical-demo-phase-diagrams.ipynb
@@ -306,7 +306,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,
diff --git a/examples/pynamical-quick-overview.ipynb b/examples/pynamical-quick-overview.ipynb
@@ -163,7 +163,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.10.4"
   }
  },
  "nbformat": 4,
diff --git a/pynamical/__init__.py b/pynamical/__init__.py
@@ -2,4 +2,4 @@
 
 from .pynamical import *
 
-__version__ = "0.3.1"
+__version__ = "0.3.2"
diff --git a/pynamical/pynamical.py b/pynamical/pynamical.py
@@ -160,7 +160,7 @@ def cubic_map(pop, rate):
     float
         scalar result of cubic map at time t+1
     """
-    return rate * pop ** 3 + pop * (1 - rate)
+    return rate * pop**3 + pop * (1 - rate)
 
 
 @jit(cache=True, nopython=True)  # pragma: no cover
@@ -180,7 +180,7 @@ def singer_map(pop, rate):
     float
         scalar result of singer map at time t+1
     """
-    return rate * (7.86 * pop - 23.31 * pop ** 2 + 28.75 * pop ** 3 - 13.3 * pop ** 4)
+    return rate * (7.86 * pop - 23.31 * pop**2 + 28.75 * pop**3 - 13.3 * pop**4)
 
 
 def simulate(
@@ -436,7 +436,8 @@ def get_bifurcation_plot_points(pops):
     for rate in pops.columns:
         # append the growth rate as the x column and all the population values
         # as the y column
-        xy_points = xy_points.append(pd.DataFrame({"x": rate, "y": pops[rate]}))
+        to_append = pd.DataFrame({"x": rate, "y": pops[rate]})
+        xy_points = pd.concat([xy_points, to_append])
 
     # reset the index and drop old index before returning the xy point data
     xy_points = xy_points.reset_index().drop(labels="index", axis=1)
diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-matplotlib>=3.3
-numba>=0.52
-numpy>=1.19
-pandas>=1.1
+matplotlib>=3.5
+numba>=0.53
+numpy>=1.20,<1.22
+pandas>=1.3
diff --git a/setup.py b/setup.py
@@ -33,10 +33,9 @@
     "Topic :: Scientific/Engineering :: Information Analysis",
     "Programming Language :: Python",
     "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",
 ]
 
 # only specify install_requires if not in RTD environment
@@ -48,7 +47,7 @@
 
 setup(
     name="pynamical",
-    version="0.3.1",
+    version="0.3.2",
     description="Model, simulate, and visualize discrete nonlinear dynamical systems",
     long_description=LONG_DESCRIPTION,
     classifiers=CLASSIFIERS,
@@ -58,6 +57,6 @@
     license="MIT",
     platforms="any",
     packages=["pynamical"],
-    python_requires=">=3.6",
+    python_requires=">=3.8",
     install_requires=INSTALL_REQUIRES,
 )
diff --git a/tests/create-environment.sh b/tests/create-environment.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+set -e
+eval "$(conda shell.bash hook)"
+conda deactivate
+mamba env remove -n pynamical --yes
+mamba clean --all --yes --quiet
+mamba create -c conda-forge --strict-channel-priority -n pynamical --file "../docker/requirements.txt" --yes
+eval "$(conda shell.bash hook)"
+conda activate pynamical
+pip uninstall pynamical --yes
+pip install -e ../.
+python -m ipykernel install --sys-prefix --name pynamical --display-name "Python (pynamical)"
+mamba clean --all --yes --quiet
+mamba env export -n pynamical > environment.yml
+mamba list
+jupyter kernelspec list
+ipython -c "import pynamical; print('pynamical version', pynamical.__version__)"
diff --git a/tests/environment-dev.yml b/tests/environment-dev.yml
@@ -14,7 +14,7 @@ dependencies:
     - jupyterlab
 
     # linting/testing
-    - black
+    - black=22.*
     - coverage
     - flake8
     - flake8-bugbear
diff --git a/tests/environment.yml b/tests/environment.yml

Original file line number	Diff line number	Diff line change
`@@ -450,7 +450,7 @@`
`450`	`450`	`"name": "python",`
`451`	`451`	`"nbconvert_exporter": "python",`
`452`	`452`	`"pygments_lexer": "ipython3",`
`453`		`- "version": "3.8.6"`
	`453`	`+ "version": "3.10.4"`
`454`	`454`	`}`
`455`	`455`	`},`
`456`	`456`	`"nbformat": 4,`
Original file line number	Diff line number	Diff line change
`@@ -233,7 +233,7 @@`
`233`	`233`	`"name": "python",`
`234`	`234`	`"nbconvert_exporter": "python",`
`235`	`235`	`"pygments_lexer": "ipython3",`
`236`		`- "version": "3.8.6"`
	`236`	`+ "version": "3.10.4"`
`237`	`237`	`}`
`238`	`238`	`},`
`239`	`239`	`"nbformat": 4,`
Original file line number	Diff line number	Diff line change
`@@ -295,7 +295,7 @@`
`295`	`295`	`"name": "python",`
`296`	`296`	`"nbconvert_exporter": "python",`
`297`	`297`	`"pygments_lexer": "ipython3",`
`298`		`- "version": "3.8.6"`
	`298`	`+ "version": "3.10.4"`
`299`	`299`	`}`
`300`	`300`	`},`
`301`	`301`	`"nbformat": 4,`
Original file line number	Diff line number	Diff line change
`@@ -214,7 +214,7 @@`
`214`	`214`	`"name": "python",`
`215`	`215`	`"nbconvert_exporter": "python",`
`216`	`216`	`"pygments_lexer": "ipython3",`
`217`		`- "version": "3.8.6"`
	`217`	`+ "version": "3.10.4"`
`218`	`218`	`}`
`219`	`219`	`},`
`220`	`220`	`"nbformat": 4,`
Original file line number	Diff line number	Diff line change
`@@ -306,7 +306,7 @@`
`306`	`306`	`"name": "python",`
`307`	`307`	`"nbconvert_exporter": "python",`
`308`	`308`	`"pygments_lexer": "ipython3",`
`309`		`- "version": "3.8.6"`
	`309`	`+ "version": "3.10.4"`
`310`	`310`	`}`
`311`	`311`	`},`
`312`	`312`	`"nbformat": 4,`