feat: update and cleaned envs

biosimulators · Nov 6, 2024 · 6933742 · 6933742
1 parent a95dccb
commit 6933742
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Showing 6 changed files with 83 additions and 329 deletions.
diff --git a/api/Dockerfile-api b/api/Dockerfile-api
@@ -5,16 +5,17 @@ FROM ghcr.io/biosimulators/bio-compose-server-base:latest
 
 SHELL ["/usr/bin/env", "bash", "-c"]
 
-COPY ./ ./
+COPY ./ .
 
 EXPOSE 3001
 
 RUN source ~/.bashrc \
-    && conda env update -n server -f environment.api.yml \
+    && conda env update -n server -f config/environment.api.yml \
+    && conda run pip install -e . \
     && conda clean --all --json -y
 
 # RUN source ~/.bashrc \
 #     && poetry install --without=composition,dev,worker --no-cache
 
-ENTRYPOINT ["bash", "-c", "source ~/.bashrc && uvicorn main:app --host 0.0.0.0 --port 3001 --reload"]
+ENTRYPOINT ["bash", "-c", "source ~/.bashrc && conda run uvicorn main:app --host 0.0.0.0 --port 3001 --reload"]
 
diff --git a/api/config/env.api.yml b/api/config/env.api.yml
@@ -0,0 +1,67 @@
+name: server
+channels:
+  - defaults
+  - https://repo.anaconda.com/pkgs/main
+  - https://repo.anaconda.com/pkgs/r
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=5.1
+  - bzip2=1.0.8
+  - ca-certificates=2024.9.24
+  - ld_impl_linux-64=2.40
+  - libffi=3.4.4
+  - libgcc-ng=11.2.0
+  - libgomp=11.2.0
+  - libstdcxx-ng=11.2.0
+  - libuuid=1.41.5
+  - ncurses=6.4
+  - openssl=3.0.15
+  - python=3.10.15
+  - readline=8.2
+  - setuptools=75.1.0
+  - sqlite=3.45.3
+  - tk=8.6.14
+  - tzdata=2024b
+  - wheel=0.44.0
+  - xz=5.4.6
+  - zlib=1.2.13
+  - pip:
+      - annotated-types==0.7.0
+      - anyio==4.6.2.post1
+      - cachetools==5.5.0
+      - certifi==2024.8.30
+      - charset-normalizer==3.4.0
+      - click==8.1.7
+      - dnspython==2.7.0
+      - exceptiongroup==1.2.2
+      - fastapi==0.115.4
+      - google-api-core==2.22.0
+      - google-auth==2.35.0
+      - google-cloud-core==2.4.1
+      - google-cloud-storage==2.18.2
+      - google-crc32c==1.6.0
+      - google-resumable-media==2.7.2
+      - googleapis-common-protos==1.65.0
+      - h11==0.14.0
+      - idna==3.10
+      - pip==24.3.1
+      - proto-plus==1.25.0
+      - protobuf==5.28.3
+      - pyasn1==0.6.1
+      - pyasn1-modules==0.4.1
+      - pydantic==2.9.2
+      - pydantic-core==2.23.4
+      - pydantic-settings==2.6.1
+      - pymongo==4.10.1
+      - python-dotenv==1.0.1
+      - python-multipart==0.0.17
+      - pyyaml==6.0.2
+      - requests==2.32.3
+      - requests-toolbelt==1.0.0
+      - rsa==4.9
+      - sniffio==1.3.1
+      - starlette==0.41.2
+      - toml==0.10.2
+      - typing-extensions==4.12.2
+      - urllib3==2.2.3
+      - uvicorn==0.32.0
diff --git a/api/config/environment.api.yml b/api/config/environment.api.yml
@@ -4,64 +4,10 @@ channels:
   - https://repo.anaconda.com/pkgs/main
   - https://repo.anaconda.com/pkgs/r
 dependencies:
-  - _libgcc_mutex=0.1
-  - _openmp_mutex=5.1
-  - bzip2=1.0.8
-  - ca-certificates=2024.9.24
-  - ld_impl_linux-64=2.40
-  - libffi=3.4.4
-  - libgcc-ng=11.2.0
-  - libgomp=11.2.0
-  - libstdcxx-ng=11.2.0
-  - libuuid=1.41.5
-  - ncurses=6.4
-  - openssl=3.0.15
-  - python=3.10.15
-  - readline=8.2
-  - setuptools=75.1.0
-  - sqlite=3.45.3
-  - tk=8.6.14
-  - tzdata=2024b
-  - wheel=0.44.0
-  - xz=5.4.6
-  - zlib=1.2.13
+  - pip
+  - python=3.10
   - pip:
-      - annotated-types==0.7.0
-      - anyio==4.6.2.post1
-      - cachetools==5.5.0
-      - certifi==2024.8.30
-      - charset-normalizer==3.4.0
-      - click==8.1.7
-      - dnspython==2.7.0
-      - exceptiongroup==1.2.2
-      - fastapi==0.115.4
-      - google-api-core==2.22.0
-      - google-auth==2.35.0
-      - google-cloud-core==2.4.1
-      - google-cloud-storage==2.18.2
-      - google-crc32c==1.6.0
-      - google-resumable-media==2.7.2
-      - googleapis-common-protos==1.65.0
-      - h11==0.14.0
-      - idna==3.10
-      - pip==24.3.1
-      - proto-plus==1.25.0
-      - protobuf==5.28.3
-      - pyasn1==0.6.1
-      - pyasn1-modules==0.4.1
       - pydantic==2.9.2
-      - pydantic-core==2.23.4
       - pydantic-settings==2.6.1
-      - pymongo==4.10.1
-      - python-dotenv==1.0.1
-      - python-multipart==0.0.17
       - pyyaml==6.0.2
-      - requests==2.32.3
-      - requests-toolbelt==1.0.0
-      - rsa==4.9
-      - sniffio==1.3.1
-      - starlette==0.41.2
-      - toml==0.10.2
-      - typing-extensions==4.12.2
-      - urllib3==2.2.3
       - uvicorn==0.32.0
diff --git a/assets/docker/config/environment.base.yml b/assets/docker/config/environment.base.yml
@@ -4,27 +4,8 @@ channels:
   - https://repo.anaconda.com/pkgs/main
   - https://repo.anaconda.com/pkgs/r
 dependencies:
-  - _libgcc_mutex=0.1
-  - _openmp_mutex=5.1
-  - bzip2=1.0.8
-  - ca-certificates=2024.9.24
-  - ld_impl_linux-64=2.40
-  - libffi=3.4.4
-  - libgcc-ng=11.2.0
-  - libgomp=11.2.0
-  - libstdcxx-ng=11.2.0
-  - libuuid=1.41.5
-  - ncurses=6.4
-  - openssl=3.0.15
-  - python=3.10.15
-  - readline=8.2
-  - setuptools=75.1.0
-  - sqlite=3.45.3
-  - tk=8.6.14
-  - tzdata=2024b
-  - wheel=0.44.0
-  - xz=5.4.6
-  - zlib=1.2.13
+  - pip
+  - python=3.10
   - pip:
       - annotated-types==0.7.0
       - anyio==4.6.2.post1

diff --git a/worker/Dockerfile-worker b/worker/Dockerfile-worker
@@ -5,31 +5,13 @@ FROM ghcr.io/biosimulators/bio-compose-server-base:latest
 
 SHELL ["/usr/bin/env", "bash", "-c"]
 
-COPY ./ ./
+COPY ./ .
 # COPY ../assets/docker/config/environment.base.yml ../assets/docker/config/environment.worker.yml .
 
 ENV TEST_SBML_FP="test_fixtures/Elowitz-Nature-2000-Repressilator/BIOMD0000000012_url.xml" \
     TEST_PSC_FP="/Pysces/psc/BIOMD0000000012_url.xml.psc" \
     TEST_OMEX_FP="test_fixtures/Elowitz-Nature-2000-Repressilator.omex"
 
-# os deps
-# RUN source ~/.bashrc \
-#     && apt-get update  \
-#     && apt-get install -y \
-#     meson \
-#     g++ \
-#     gfortran \
-#     libblas-dev \
-#     liblapack-dev \
-#     libgfortran5 \
-#     && conda install -c conda-forge -c pysces pysces -y \
-# 	&& conda env update -n conda-env -f config/environment.worker.yml \
-#     && poetry install --only=worker --no-cache \
-#     && rm -rf config \
-#     && rm -rf /var/lib/apt/lists/* \
-#     && apt-get autoremove -y \
-#     && apt-get clean
-
 # TODO: perhaps run --no-install-recommends?
 RUN source ~/.bashrc \
     && apt-get update  \
@@ -63,7 +45,8 @@ RUN source ~/.bashrc \
     libboost-chrono-dev \
     libboost-math-dev \
     libboost-serialization-dev \
-    && conda env update -n server -f environment.worker.yml \
+    && conda env update -n server -f config/environment.worker.yml \
+    && conda run pip install -e . \
     && rm -rf /var/lib/apt/lists/* \
     && apt-get autoremove -y \
     && apt-get clean \
@@ -74,7 +57,7 @@ RUN source ~/.bashrc \
 # && conda install "numpy<1.22.0" \
 # && conda run pip install amici biosimulators-amici --root-user-action=ignore \
 # && rm -rf config \
-ENTRYPOINT ["bash", "-c", "source ~/.bashrc && python3 main.py"]
+ENTRYPOINT ["bash", "-c", "source ~/.bashrc && conda run python3 main.py"]
 
 # --root-user-action=ignore
 #############################