Release new version in pypi (#285)

* Adds a more descriptive error for isolation

* Updates version and requirements for pypi

* Updates version and tests pypi deployment

* Adds egg to gitignore, changes project name

* Updates names of the actions to reflect which ones work on py vs conda

* Updates the name of the project to poli-base for pypi

* Updates the name of the project to poli-core

.github/workflows/python-tox-testing-base.yml

@@ -1,4 +1,4 @@
-name: poli base (conda, py3.10)
+name: poli base (py3.10)
 
 on:
   push:

.github/workflows/python-tox-testing-dockstring-env.yml

@@ -1,4 +1,4 @@
-name: poli dockstring (conda, py3.10)
+name: poli dockstring (py3.10)
 
 on:
   push:

.github/workflows/python-tox-testing-lambo-env.yml

@@ -1,4 +1,4 @@
-name: poli lambo (conda, py3.10)
+name: poli lambo (py3.10)
 
 on:
   push:

.github/workflows/python-tox-testing-protein-env.yml

@@ -1,4 +1,4 @@
-name: poli protein (conda, py3.10)
+name: poli protein (py3.10)
 
 on:
   push:

.github/workflows/python-tox-testing-rmf-env.yml

@@ -1,4 +1,4 @@
-name: poli rmf (conda, py3.10)
+name: poli rmf (py3.10)
 
 on:
   push:

.github/workflows/python-tox-testing-tdc-env.yml

@@ -1,4 +1,4 @@
-name: poli tdc (conda, py3.10)
+name: poli tdc (py3.10)
 
 on:
   push:

.gitignore

@@ -2,7 +2,7 @@
 __pycache__
 .idea
 /src/poli/config.rc
-src/poli.egg-info/
+*.egg-info/
 temp
 build
 .tox

CITATION.cff

@@ -8,6 +8,6 @@ authors:
 - family-names: "Michael"
   given-names: "Richard"
 title: "poli: a libary of discrete sequence objectives"
-version: 1.0.0.dev13
+version: 1.0.1
 date-released: 2024-01-23
 url: "https://github.com/MachineLearningLifeScience/poli"

pyproject.toml

@@ -3,11 +3,11 @@ requires = ["setuptools<=68"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "poli"
-version = "1.0.0.dev14"
+name = "poli-core"
+version = "1.0.1"
 description = "poli, a library of discrete objective functions"
 readme = "README.md"
-authors = [{name="Miguel González-Duque", email="[email protected]"}, {name="Simon Bartels"}]
+authors = [{name="Miguel González-Duque", email="[email protected]"}, {name="Simon Bartels", email="[email protected]"}]
 license = {file = "LICENSE"}
 classifiers = [
     "License :: OSI Approved :: MIT License",
@@ -19,13 +19,17 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Chemistry",
     "Topic :: Scientific/Engineering :: Mathematics",
     "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Development Status :: 3 - Alpha",
+    "Operating System :: MacOS",
+    "Operating System :: Unix",
 ]
 keywords = ["optimization", "molecular", "discrete", "proteins"]
 dependencies = [
     "numpy<2",
     "rdkit",
     "selfies"
 ]
+requires-python = ">=3.9"
 
 [project.optional-dependencies]
 foldx = [
@@ -79,7 +83,7 @@ profile = "black"
 exclude = ["src/poli/core/util/proteins/rasp/inner_rasp", "src/poli/objective_repository/gfp_cbas"]
 
 [tool.bumpversion]
-current_version = "1.0.0.dev13"
+current_version = "1.0.1"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

setup.cfg

@@ -1,15 +1,24 @@
 [metadata]
-name = poli
-version = "1.0.0.dev13"
+name = poli-core
+version = "1.0.1"
 author = Miguel González-Duque
 author_email = [email protected]
 description = A library of discrete objective functions
 long_description = file: README.md
 long_description_content_type = text/markdown
 classifiers =
-    Programming Language :: Python :: 3
     License :: OSI Approved :: MIT License
-    Operating System :: OS Independent
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Intended Audience :: Education
+    Intended Audience :: Science/Research
+    Topic :: Scientific/Engineering :: Bio-Informatics
+    Topic :: Scientific/Engineering :: Chemistry
+    Topic :: Scientific/Engineering :: Mathematics
+    Topic :: Scientific/Engineering :: Artificial Intelligence
+    Development Status :: 3 - Alpha
+    Operating System :: MacOS
+    Operating System :: Unix
 
 [options]
 package_dir =

src/poli/__init__.py

@@ -1,6 +1,6 @@
 """poli, a library for discrete black-box objective functions."""
 
-__version__ = "1.0.0.dev13"
+__version__ = "1.0.1"
 from .core.util.isolation.instancing import instance_function_as_isolated_process
 
 # from .core import get_problems

src/poli/core/util/isolation/instancing.py

@@ -311,11 +311,12 @@ def instance_function_as_isolated_process(
     # Check if the user has conda installed
     if shutil.which("conda") is None:
         raise RuntimeError(
-            "Conda is not installed. For poli's isolation mechanisms to work, "
+            "Conda is not installed/not in the PATH. For poli's isolation mechanisms to work, \n"
             "we need conda to be installed.\n"
-            "If you are not interested in using conda, you can install all the "
+            "If you are not interested in using conda, you can install all the \n"
             "relevant dependencies for black boxes using pip and optional arguments.\n"
-            "Check the documentation of the black box you are interested in for more information."
+            "Check the documentation of the black box you are interested in for more information.\n"
+            "https://machinelearninglifescience.github.io/poli-docs/."
         )
 
     # Register the problem if it hasn't been registered.

tox.ini

@@ -89,7 +89,7 @@ commands=
     pytest {tty:--color=yes} -v -m "not slow and poli__dockstring" {posargs}
 
 [testenv:poli-rasp-py310]
-description = run the tests with pytest on the RaSP environment for poli
+description = run the tests with pytest and conda on the RaSP environment for poli
 basepython = python3.10
 wheel_build_env = .pkg
 deps=
@@ -122,7 +122,4 @@ deps=
     -r requirements.txt
     -e.[ehrlich]
 commands=
-    sh -c 'if conda info --envs | grep -q poli__ehrlich_holo; then echo "poli__ehrlich_holo already exists"; else conda env create -f ./src/poli/objective_repository/ehrlich_holo/environment.yml; fi'
-    sh -c "conda run -n poli__ehrlich_holo python -m pip uninstall -y poli"
-    sh -c "conda run -n poli__ehrlich_holo python -m pip install -e ."
     pytest {tty:--color=yes} -v -m 'not slow and poli__ehrlich_holo' {posargs}