Update python version support (#477)

* Add arviz-dependency to requirements

* Include InferenceData-object to results

* Fix 085 (#465)

* add __init__.py to elfi/methods/bsl/

* Update CHANGELOG.rst

* Bump version (#466)

* Clean up inference data-object wrapper

* Update CHANGELOG

* Fix typo

* Update info on supported Python versions.

* Fix error caused by new version of numpy

* Enable maxiter option

* Remove forgotten print-commands

* Remove arviz-elements

* Remove arviz dependency

* Include setuptools in requirements

Author: hpesonen

.github/workflows/pytest.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v2

CHANGELOG.rst

@@ -1,6 +1,7 @@
 Changelog
 =========
 
+- Drop official Python support for 3.7 and 3.8 as GPy is not officially supported for these versions
 - Enable using `maxiter` in `bo.utils.minimize`
 - Fix surrogate model copy operation
 - Fix typo in requirements.txt

CONTRIBUTING.rst

@@ -72,16 +72,16 @@ Ready to contribute? Here's how to set up `ELFI` for local development.
 3. Make sure you have `Python 3 <https://www.python.org/>`_ and
    `Anaconda Distribution <https://www.anaconda.com/>`_ installed on your
    machine. Check your conda and Python versions. Currently supported Python versions
-   are 3.7, 3.8, 3.9, 3.10::
+   are 3.9, 3.10, 3.11, 3.12::
 
    $ conda -V
    $ python -V
 
 4. Install your local copy and the development requirements into a conda
-   environment. You may need to replace "3.7" in the first line with the python
+   environment. You may need to replace "3.9" in the first line with the python
    version printed in the previous step::
 
-    $ conda create -n elfi python=3.7 numpy
+    $ conda create -n elfi python=3.9 numpy
     $ source activate elfi
     $ cd elfi
     $ make dev
@@ -136,7 +136,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.md.
-3. The pull request should work for Python 3.7 and later. Check
+3. The pull request should work for Python 3.9 and later. Check
    https://github.com/elfi-dev/elfi/actions/workflows/pytest.yml
    and make sure that the tests pass for all supported Python versions.
 

README.md

@@ -44,7 +44,7 @@ is preferable.
 Installation with pip
 ---------------------
 
-ELFI requires Python 3.7 or greater. You can install ELFI by typing in your terminal:
+ELFI requires Python 3.9 or greater. You can install ELFI by typing in your terminal:
 
 ```
 pip install elfi
@@ -95,7 +95,7 @@ with your default Python environment and can easily use different versions of Py
 in different projects. You can create a virtual environment for ELFI using anaconda with:
 
 ```
-conda create -n elfi python=3.7 numpy
+conda create -n elfi python=3.9 numpy
 source activate elfi
 pip install elfi
 ```
@@ -125,7 +125,7 @@ Resolving these may sometimes go wrong:
 - If you receive an error about `yaml.load`, install `pyyaml`.
 - On OS X with Anaconda virtual environment say `conda install python.app` and then use
 `pythonw` instead of `python`.
-- Note that ELFI requires Python 3.7 or greater so try `pip3 install elfi`.
+- Note that ELFI requires Python 3.9 or greater so try `pip3 install elfi`.
 - Make sure your Python installation meets the versions listed in `requirements.txt`.
 
 

docs/installation.rst

@@ -3,7 +3,7 @@
 Installation
 ============
 
-ELFI requires Python 3.7 or greater (see below how to install). To install ELFI, simply
+ELFI requires Python 3.9 or greater (see below how to install). To install ELFI, simply
 type in your terminal:
 
 .. code-block:: console
@@ -18,16 +18,16 @@ process.
 .. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
 
 
-Installing Python 3.7
+Installing Python 3.9
 ---------------------
 
 If you are new to Python, perhaps the simplest way to install it is with Anaconda_ that
-manages different Python versions. After installing Anaconda, you can create a Python 3.7.
+manages different Python versions. After installing Anaconda, you can create a Python 3.9.
 environment with ELFI:
 
 .. code-block:: console
 
-    conda create -n elfi python=3.7 numpy
+    conda create -n elfi python=3.9 numpy
     source activate elfi
     pip install elfi
 
@@ -51,7 +51,7 @@ Resolving these may sometimes go wrong:
 * If you receive an error about missing ``numpy``, please install it first.
 * If you receive an error about `yaml.load`, install ``pyyaml``.
 * On OS X with Anaconda virtual environment say `conda install python.app` and then use `pythonw` instead of `python`.
-* Note that ELFI requires Python 3.7 or greater
+* Note that ELFI requires Python 3.9 or greater
 * In some environments ``pip`` refers to Python 2.x, and you have to use ``pip3`` to use the Python 3.x version
 * Make sure your Python installation meets the versions listed in requirements_.
 

docs/quickstart.rst

@@ -3,7 +3,7 @@ Quickstart
 
 First ensure you have
 `installed <http://elfi.readthedocs.io/en/stable/installation.html>`__
-Python 3.7 (or greater) and ELFI. After installation you can start using
+Python 3.9 (or greater) and ELFI. After installation you can start using
 ELFI:
 
 .. code:: ipython3

elfi/examples/bdm.py

@@ -25,10 +25,11 @@ def prepare_inputs(*inputs, **kwinputs):
     """
     alpha, delta, tau, N = inputs
     meta = kwinputs['meta']
-
     # Organize the parameters to an array. The broadcasting works nicely with constant
     # arguments.
-    param_array = np.row_stack(np.broadcast(alpha, delta, tau, N))
+    param_array = np.row_stack(
+        [(a, d, t, N) for (a, d, t, N) in np.broadcast(alpha, delta, tau, N)]
+        )
 
     # Prepare a unique filename for parallel settings
     filename = '{model_name}_{batch_index}_{submission_index}.txt'.format(**meta)
@@ -37,7 +38,6 @@ def prepare_inputs(*inputs, **kwinputs):
     # Add the filenames to kwinputs
     kwinputs['filename'] = filename
     kwinputs['output_filename'] = filename[:-4] + '_out.txt'
-
     # Return new inputs that the command will receive
     return inputs, kwinputs
 
@@ -71,7 +71,7 @@ def process_result(completed_process, *inputs, **kwinputs):
 def T1(clusters):
     """Summary statistic for BDM."""
     clusters = np.atleast_2d(clusters)
-    return np.sum(clusters > 0, 1) / np.sum(clusters, 1)
+    return np.sum(clusters > 0, axis=1) / np.sum(clusters, axis=1)
 
 
 def T2(clusters, n=20):

requirements.txt

@@ -1,5 +1,5 @@
 dask[distributed]>=2.30.0
-numpy>=1.12.1, <1.25
+numpy>=1.12.1
 scipy>=0.19
 matplotlib>=1.1
 GPy>=1.0.9
@@ -8,3 +8,4 @@ ipyparallel>=6
 toolz>=0.8
 scikit-learn>=0.18.1
 numdifftools>=0.9
+setuptools>=69

setup.py

@@ -31,7 +31,7 @@
     long_description=(open('docs/description.rst').read()),
     license='BSD',
     classifiers=[
-        'Programming Language :: Python :: 3.7', 'Topic :: Scientific/Engineering',
+        'Programming Language :: Python :: 3.9', 'Topic :: Scientific/Engineering',
         'Topic :: Scientific/Engineering :: Artificial Intelligence',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
         'Topic :: Scientific/Engineering :: Mathematics', 'Operating System :: OS Independent',