chore(version): 0.4.3

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>

Author: cameronraysmith

MODULE.bazel

@@ -4,7 +4,7 @@ pyrovelocity MODULE
 
 module(
     name = "pyrovelocity",
-    version = "0.4.2",
+    version = "0.4.3",
     compatibility_level = 1,
 )
 

Makefile

@@ -975,8 +975,8 @@ approve-prs: ## Approve github pull requests from bots: PR_ENTRIES="2-5 10 12-18
 		fi; \
 	done
 
-PREVIOUS_VERSION := 0.4.1
-NEXT_VERSION := 0.4.2
+PREVIOUS_VERSION := 0.4.2
+NEXT_VERSION := 0.4.3
 VERSION_FILES := \
 	pyproject.toml \
 	conda/colab/construct.yaml \

conda/colab/construct.yaml

@@ -1,5 +1,5 @@
 name: pyrovelocity-colab
-version: 0.4.2
+version: 0.4.3
 
 channels:
   - pytorch
@@ -51,7 +51,7 @@ specs:
   - aws-c-cal=0.7.1=h87b94db_1
   - aws-c-common=0.9.23=h4ab18f5_0
   - aws-c-compression=0.2.18=he027950_7
-  - aws-c-event-stream=0.4.2=h7671281_15
+  - aws-c-event-stream=0.4.3=h7671281_15
   - aws-c-http=0.8.2=he17ee6b_6
   - aws-c-io=0.14.10=h826b7d6_1
   - aws-c-mqtt=0.10.4=hcd6a914_8
@@ -249,8 +249,8 @@ specs:
   - jaraco.classes=3.4.0=pyhd8ed1ab_2
   - jaraco.context=6.0.1=pyhd8ed1ab_0
   - jaraco.functools=4.1.0=pyhd8ed1ab_0
-  - jax=0.4.26=pyhd8ed1ab_0
-  - jaxlib=0.4.26=cuda120py311had15d7a_201
+  - jax=0.4.36=pyhd8ed1ab_0
+  - jaxlib=0.4.36=cuda120py311had15d7a_201
   - jaxtyping=0.2.36=pyhd8ed1ab_0
   - jedi=0.19.2=pyhd8ed1ab_1
   - jeepney=0.9.0=pyhd8ed1ab_0
@@ -373,7 +373,7 @@ specs:
   - mashumaro=3.15=pyhd8ed1ab_1
   - matplotlib-base=3.10.1=py311h2b939e6_0
   - matplotlib-inline=0.1.7=pyhd8ed1ab_1
-  - mdit-py-plugins=0.4.2=pyhd8ed1ab_1
+  - mdit-py-plugins=0.4.3=pyhd8ed1ab_1
   - mdurl=0.1.2=pyhd8ed1ab_1
   - mistune=3.1.2=pyhd8ed1ab_0
   - mkl=2020.4=h726a3e6_304

containers/gpu.Dockerfile

@@ -77,7 +77,7 @@ COPY . /root
 # development
 RUN pip install --no-deps -e .
 # distribution
-# RUN pip install pyrovelocity==0.4.2
+# RUN pip install pyrovelocity==0.4.3
 
 ARG tag
 ENV FLYTE_INTERNAL_IMAGE $tag

containers/pkg.Dockerfile

@@ -34,7 +34,7 @@ COPY . /root
 # development
 RUN pip install --no-deps -e .
 # distribution
-# RUN pip install pyrovelocity==0.4.2
+# RUN pip install pyrovelocity==0.4.3
 
 ARG tag
 ENV FLYTE_INTERNAL_IMAGE $tag

docs/source/notebooks/pyrovelocity_colab_template.ipynb

@@ -70,7 +70,7 @@
         }
       ],
       "source": [
-        "pyrovelocity_version = \"0.4.2\"\n",
+        "pyrovelocity_version = \"0.4.3\"\n",
         "pyrovelocity_colab_script_url = (\n",
         "    \"https://storage.googleapis.com/pyrovelocity/data/scripts/\"\n",
         "    + f\"pyrovelocity-colab-{pyrovelocity_version}-Linux-x86_64.sh\"\n",

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyrovelocity"
-version = "0.4.2"
+version = "0.4.3"
 packages = [{ include = "pyrovelocity", from = "src" }]
 description = "A multivariate RNA Velocity model to estimate future cell states with uncertainty using probabilistic modeling with pyro."
 authors = ["pyrovelocity team"]
@@ -63,8 +63,8 @@ httpx = ">=0.27.0"
 h5py = ">=3.9.0"
 # hdf5plugin = ">=4.4.0"
 ibis-framework = { extras = ["duckdb"], version = ">=9.2.0" }
-jax = ">=0.4.23"
-jaxlib = ">=0.4.23"
+jax = ">=0.4.33"
+jaxlib = ">=0.4.33"
 jaxtyping = ">=0.2.25"
 leidenalg = ">=0.9.1"
 llvmlite = { version = ">=0.41.1", python = "<3.12" }
@@ -372,12 +372,12 @@ virtual_package_spec = "conda/virtual-packages.yml"
 python = ">=3.11, <3.12"
 pip = ">=23.2"
 fmt = ">=10.2.1,<11.0"
-# jax "<0.4.27" required
+# jax "<0.4.37" required
 # when using conda-lock
 # due to https://github.com/google/jax/issues/21116
-# fixed in jax 0.4.29 but not available on conda-forge
-jax = ">=0.4.23,<0.4.27"
-jaxlib = ">=0.4.23,<0.4.27"
+# fixed in jax 0.4.39 but not available on conda-forge
+jax = ">=0.4.33,<0.4.37"
+jaxlib = ">=0.4.33,<0.4.37"
 pydantic = ">=2.1.1"
 # scikit-learn requires an upper bound of
 # 1.2.0 when using conda-lock due to inconsistent

scripts/conda

@@ -3,7 +3,7 @@
 set -euo pipefail
 
 PACKAGE_NAME="pyrovelocity"
-PACKAGE_VERSION="0.4.2"
+PACKAGE_VERSION="0.4.3"
 CONDA_BUILD_STRING="pyhff70e4c"
 CONDA_BUILD_NUMBER="0"
 # CONDA_CHANNEL_LABEL="pyrovelocity_dev"
@@ -32,7 +32,7 @@ Example:
 
     ./conda \\
     --name pyrovelocity \\
-    --version 0.4.2.dev1 \\
+    --version 0.4.3.dev1 \\
     --build-string pyhff70e4c \\
     --build-number 0 \\
     --label pyrovelocity_dev
@@ -67,9 +67,9 @@ PACKAGE_SPEC="conda-forge/label/\
 $CONDA_CHANNEL_LABEL::\
 $PACKAGE_NAME=$PACKAGE_VERSION=$CONDA_BUILD_STRING"_"$CONDA_BUILD_NUMBER"
 
-BLUE="\0.4.2;34;1m"
+BLUE="\0.4.3;34;1m"
 BOLD="\033[1m"
-NO_COLOR="\0.4.2m"
+NO_COLOR="\0.4.3m"
 if [ "$USE_COLOR" = false ]; then
     BLUE=""
     BOLD=""