Repository: openpathsampling/openpathsampling (language: python)

Issue:
OpenPathSampling 1.6.1
OpenPathSampling 1.6.1 is a minor update, primarily focused on allowing OPS to run/be tested on Python 3.12. In practice, that means removing dependency on tools that prevented Python 3.12 support. In particular, this removes `nose` from our testing requirements, and deprecates our integration with PyEMMA, which is no longer maintained.

**DEPRECATION:** As of OPS 1.6.1, we no longer recommend the use of `PyEMMAFeaturizerCV`. PyEMMA is no longer maintained. Please do not create collective variables based on PyEMMA.

## Miscellaneous improvements

* Test against Python 3.12; deprecate PyEMMA ([#1145](https://github.com/openpathsampling/openpathsampling/pull/1145) #Deprecations)
* Cut off `nose` ([#1141](https://github.com/openpathsampling/openpathsampling/pull/1141) #upstream_changed)
* Fix a few more setup -> setup_method tests ([#1142](https://github.com/openpathsampling/openpathsampling/pull/1142) #upstream_changed)


Discussion / hints:

Fix patch:
diff --git a/.github/workflows/deploy_docs.yml b/.github/workflows/deploy_docs.yml
index 518d094a4..d62d14937 100644
--- a/.github/workflows/deploy_docs.yml
+++ b/.github/workflows/deploy_docs.yml
@@ -21,7 +21,7 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          python-version: "3.9"
+          python-version: "3.11"
           miniforge-variant: Mambaforge
       - name: "Install requirements"
         run: source devtools/conda_install_reqs.sh
diff --git a/openpathsampling/netcdfplus/version.py b/openpathsampling/netcdfplus/version.py
index 18fd82b09..5751a0a35 100644
--- a/openpathsampling/netcdfplus/version.py
+++ b/openpathsampling/netcdfplus/version.py
@@ -1,4 +1,4 @@
-short_version = '1.6.1.dev0'
+short_version = '1.6.2.dev0'
 version = short_version
 full_version = short_version
 git_revision = 'alpha'
diff --git a/setup.cfg b/setup.cfg
index 622f81c2c..c275e2a95 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = openpathsampling
-version = 1.6.1.dev0
+version = 1.6.2.dev0
 description = A Python package for path sampling simulations
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -30,7 +30,7 @@ python_requires = >=3.10
 install_requires = 
     future
     psutil
-    numpy
+    numpy<2.0
     scipy
     pandas
     netcdf4
@@ -45,7 +45,7 @@ install_requires =
 # required for many integrations with other packages
 # dill and sqlalchemy are technically only required for Python 3.11+, but
 # we'll include them for all Python versions
-packages = find:
+packages = find_namespace:
 
 [options.extras_require]
 test = 
@@ -55,6 +55,3 @@ test =
     nbval>=0.10.0
 simstore =
     # simstore requirements have been moved to main
-
-[bdist_wheel]
-universal = 1


Test patch:
diff --git a/.autorelease/test-testpypi b/.autorelease/test-testpypi
index f1fc4c695..66922ce52 100644
--- a/.autorelease/test-testpypi
+++ b/.autorelease/test-testpypi
@@ -1,4 +1,5 @@
 #!/bin/bash
 
 python -m pip install pytest sqlalchemy
+python -c "import openpathsampling"
 py.test --pyargs openpathsampling.tests