Updated the toffy environment file (#434)

* added a dev-environment, updated environment.yml

* updated python version to 3.11 for the environment.yml files

* added release and prerelese environments

* updated mibi-bin-tools and alpineer

* updated lock file

* added pywavelets

* mibi-bin-tools 0.2.12

* pymzq is not compatible with python 3.12

* set CI to python 3.11

* set latest python version, trying CI with python 3.12 again

* 3.x python

* updated pyproject.toml

* I see why I set it back to Python 3.11 now

* removed python 3.12 classifier

.github/workflows/build.yml

@@ -14,7 +14,7 @@ jobs:
       # Ensure that a wheel builder finishes even if another fails
       fail-fast: false
       matrix:
-        python-version: [3.x]
+        python-version: [3.11]
         poetry-version: [latest]
 
     steps:

.github/workflows/test.yml

@@ -14,7 +14,7 @@ jobs:
       # Ensure that a wheel builder finishes even if another fails
       fail-fast: false
       matrix:
-        python-version: [3.x] # latest stable release
+        python-version: [3.11] # latest stable release
         poetry-version: [latest]
 
     steps:

.gitignore

@@ -141,3 +141,4 @@ scripts/
 coverage.lcov
 
 data/combined/*.csv
+.idea/

prerelease-environment.yml

@@ -0,0 +1,17 @@
+name: toffy_prerelease_env
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - pip
+  - numpy
+  - seaborn
+  - scikit-learn
+  - jupyterlab
+  - pip:
+    - natsort
+    - watchdog
+    - alpineer==0.1.10
+    - mibi-bin-tools==0.2.11
+    - jupyter_contrib_nbextensions
+    - -e .

pyproject.toml

@@ -36,9 +36,9 @@ style = "pep440"
 metadata = false
 
 [tool.poetry.dependencies]
-python = ">=3.9,<3.12"
+python = "^3.9,<3.12"
 alpineer = ">=0.1.9"
-mibi-bin-tools = "0.2.11"
+mibi-bin-tools = "0.2.12"
 ipywidgets = "^8"
 numpy = "1.*"
 natsort = "^8"
@@ -48,6 +48,7 @@ watchdog = "^3"
 tqdm = "^4"
 scipy = "^1.10.1"
 pandas = "^2"
+pywavelets = "^1.4.1"
 
 [tool.poetry.group.test]
 optional = true

environment.yml → release-environment.yml

@@ -2,7 +2,7 @@ name: toffy_env
 channels:
   - conda-forge
 dependencies:
-  - python=3.9
+  - python=3.11
   - pip
   - numpy
   - seaborn
@@ -11,7 +11,7 @@ dependencies:
   - pip:
     - natsort
     - watchdog
-    - alpineer==0.1.7
-    - mibi-bin-tools==0.2.9
-    - toffy==0.2.0
+    - alpineer==0.1.10
+    - mibi-bin-tools==0.2.11
     - jupyter_contrib_nbextensions
+    - toffy==0.2.1