Upgrade to Numpy 2

Dockerfile

@@ -31,8 +31,9 @@ RUN wget --quiet https://github.com/Kitware/CMake/releases/download/v${CMAKE_VER
 
 ENV PATH $PATH:$PWD/cmake-${CMAKE_VERSION}-linux-x86_64/bin/
 
-# Copy the environment yaml to cache environment when possible
+# Copy the environment yaml and requirements.txt to cache environment when possible
 COPY environment.yml /code/timemachine/
+COPY requirements.txt /code/timemachine/
 
 WORKDIR /code/timemachine/
 
@@ -50,10 +51,6 @@ ENV CONDA_DEFAULT_ENV ${ENV_NAME}
 
 WORKDIR /code/
 
-# Copy the pip requirements to cache when possible
-COPY requirements.txt /code/timemachine/
-RUN pip install --no-cache-dir -r timemachine/requirements.txt
-
 # NOTE: timemachine_ci must come before timemachine in the Dockerfile;
 # otherwise, CI will try (and fail) to build timemachine to reach the
 # timemachine_ci target

environment.yml

@@ -5,6 +5,5 @@ dependencies:
   - python=3.12.8
   - jax=0.4.28
   - jaxlib=0.4.28=cpu*
-  # Include numpy/scipy to reduce the size of the Docker container
-  - numpy=1.26.4
-  - scipy=1.15.1
+  - pip:
+    - -r requirements.txt

requirements.txt

@@ -1,8 +1,8 @@
-numpy==1.26.4
+numpy==2.2.2
 scipy==1.15.1
 pymbar==3.1.0
 networkx==2.8.8
-matplotlib==3.7.1
+matplotlib==3.10.0
 rdkit==2024.9.4
 --extra-index-url https://pypi.anaconda.org/OpenEye/simple
 openeye-toolkits==2020.2.0

timemachine/cpp/CMakeLists.txt

@@ -44,7 +44,7 @@ set(LIBRARY_NAME custom_ops)
 set(PYBIND_SRC_DIR pybind11)
 
 if(NOT EXISTS ${PYBIND_SRC_DIR})
-  execute_process(COMMAND git clone --depth 1 --branch v2.9.2 https://github.com/pybind/pybind11.git ${PYBIND_SRC_DIR})
+  execute_process(COMMAND git clone --depth 1 --branch v2.13.6 https://github.com/pybind/pybind11.git ${PYBIND_SRC_DIR})
 endif()
 
 set(EIGEN_SRC_DIR eigen)