Merge pull request #83 from marius311/pkgext

Use 1.9 package extensions

.dockerignore

@@ -1,6 +1,9 @@
 *
 !src
+!ext
+!dat
 !Project.toml
+!CondaPkg.toml
 !README.md
 !docs
 **/.ipynb_checkpoints

.github/workflows/runtests.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: ['1.7', '1.8', '^1.9.0-0']
+        julia-version: ['1.8', '^1.9.0-0']
         os: [ubuntu-latest]
         provider: ['mkl', 'fftw']
       fail-fast: false
@@ -16,13 +16,13 @@ jobs:
 
     steps:
       - uses: actions/checkout@v1.0.0
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia-version }}
       - run: >
           sudo apt-get install --no-install-recommends gfortran python3-setuptools python3-wheel
           && pip3 install camb healpy
           && julia -e 'using Pkg; Pkg.add(url="https://github.com/EthanAnderes/CirculantCov.jl")'
           && julia --project .github/set_fftw_provider.jl "${{ matrix.provider }}"
-      - uses: julia-actions/julia-runtest@master
+      - uses: julia-actions/julia-runtest@v1
         timeout-minutes: 30

CondaPkg.toml

@@ -0,0 +1,3 @@
+
+[pip.deps]
+camb = ""

Dockerfile

@@ -20,7 +20,9 @@ RUN apt-get update \
         libsqlite3-dev \
         nodejs \
         npm \
-        python-openssl \
+        python3 \
+        python3-pip \
+        python3-openssl \
         tk-dev \
         wget \
         xz-utils \
@@ -29,7 +31,7 @@ RUN apt-get update \
 
 ## install julia
 RUN mkdir /opt/julia \
-    && curl -L https://julialang-s3.julialang.org/bin/linux/x64/1.8/julia-1.8.5-linux-x86_64.tar.gz | tar zxf - -C /opt/julia --strip=1 \
+    && curl -L https://julialang-s3.julialang.org/bin/linux/x64/1.9/julia-1.9.0-rc2-linux-x86_64.tar.gz | tar zxf - -C /opt/julia --strip=1 \
     && chown -R 1000 /opt/julia \
     && ln -s /opt/julia/bin/julia /usr/local/bin
 
@@ -39,40 +41,21 @@ ARG NB_UID=1000
 ENV USER $NB_USER
 ENV NB_UID $NB_UID
 ENV HOME /home/$NB_USER
+ENV PATH=$HOME/.local/bin:$PATH
 RUN adduser --disabled-password --gecos "Default user" --uid $NB_UID $NB_USER
 USER $NB_USER
 
-## pyenv
-# install python with pyenv since we need a dynamically-linked executable so
-# that PyJulia works
-ENV PATH="$HOME/.pyenv/shims:$HOME/.pyenv/bin:$PATH"
-RUN curl https://pyenv.run | bash \
-    && CFLAGS="-O2" PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.13 \
-    && pyenv global 3.9.13
-
 ## install Python packages
 # see https://github.com/jupyter/jupyter_client/issues/637 re: jupyter-client==6.1.12
-RUN pip install --no-cache-dir \
-        cython \
+RUN pip3 install --no-cache-dir \
         "jinja2<3.1.0" \
-        julia \
+        juliacall \
         "jupyterlab>=3" \
-        jupyter-client==6.1.12 \
         jupytext \
         matplotlib \
         "nbconvert<6" \
-        numpy \
-        scipy \
-        setuptools \
     && rm -rf $HOME/.cache
 
-## install CAMB
-RUN mkdir -p $HOME/src/camb \
-    && curl -L https://github.com/cmbant/camb/tarball/e8184bb | tar zxf - -C $HOME/src/camb --strip=1 \
-    && cd $HOME/src/camb \
-    && NONNATIVE=1 python setup.py make install 
-
-
 ## build args
 # build with PRECOMPILE=0 and/or PACKAGECOMPILE=0 to skip precompilation steps,
 # which makes for a quicker build but slower startup (mostly useful for
@@ -88,13 +71,15 @@ ARG JULIA_FFTW_PROVIDER=FFTW
 # to improve Docker caching, we first precompile dependencies by copying in
 # Project.toml (and making a dummy src/CMBLensing.jl which we have to), so that
 # other changes to files in src/ won't have to redo these steps
-COPY --chown=1000 Project.toml $HOME/CMBLensing/
+COPY --chown=1000 Project.toml CondaPkg.toml $HOME/CMBLensing/
 COPY --chown=1000 docs/Project.toml $HOME/CMBLensing/docs/
 RUN mkdir $HOME/CMBLensing/src && mkdir $HOME/CMBLensing/docs/build && touch $HOME/CMBLensing/src/CMBLensing.jl
 ENV JULIA_PROJECT=$HOME/CMBLensing/docs
 RUN JULIA_PKG_PRECOMPILE_AUTO=0 julia -e 'using Pkg; pkg"status; dev ~/CMBLensing; instantiate"' \
     && rm -rf $HOME/.julia/conda/3/pkgs
 COPY --chown=1000 src $HOME/CMBLensing/src
+COPY --chown=1000 ext $HOME/CMBLensing/ext
+COPY --chown=1000 dat $HOME/CMBLensing/dat
 RUN (test $PRECOMPILE = 0 || julia -e 'using Pkg; pkg"precompile"')
 
 
@@ -111,6 +96,7 @@ COPY --chown=1000 docs/src $HOME/CMBLensing/docs/src
 COPY --chown=1000 docs/ipython_config.py $HOME/.ipython/profile_default/ipython_config.py
 WORKDIR $HOME/CMBLensing/docs/src
 ARG RUNDOCS=1
+
 RUN jupytext --to notebook *.md \
     && rm *.md \
     && find . -not -name "*gpu*" -name "*.ipynb" \

Project.toml

@@ -7,11 +7,10 @@ version = "0.10.0"
 AbstractFFTs = "621f4979-c628-5d54-868e-fcf4e3e8185c"
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 Bijections = "e2ed5e7c-b2de-5872-ae92-c73ca462fb04"
-CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
-CUDAKernels = "72cfdca4-0801-4ab0-bf6a-d52aa10adc57"
 ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2"
 CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
+ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
 CompositeStructs = "534720e6-2374-40c5-8712-bf9a2f1643c6"
 CoordinateTransformations = "150eb455-5306-5404-9cee-2592286d6298"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
@@ -32,11 +31,11 @@ Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 KahanSummation = "8e2b3108-d4c1-50be-a7a2-16352aec75c3"
-KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 Lazy = "50d2b5c4-7a5e-59d5-8109-a42b560f39c0"
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Loess = "4345ca2d-374a-55d4-8d30-97f9976e7612"
+MCMCDiagnosticTools = "be115224-59cd-429b-ad48-344e309966f0"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
 Match = "7eb4fadd-790c-5f42-8a69-bfa0b872bfbf"
@@ -51,7 +50,6 @@ PlotUtils = "995b91a9-d308-5afd-9ec6-746e21dbc043"
 Preferences = "21216c6a-2e73-6563-6e65-726566657250"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
@@ -70,11 +68,24 @@ Tullio = "bc48ee85-29a4-5162-ae0b-a64e1601d4bc"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
+[weakdeps]
+CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
+CUDAKernels = "72cfdca4-0801-4ab0-bf6a-d52aa10adc57"
+KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
+MuseInference = "43b88160-90c7-4f71-933b-9d65205cd921"
+PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
+PythonPlot = "274fc56d-3b97-40fa-a1cd-1b4a50311bf9"
+
+[extensions]
+CMBLensingCUDAExt = "CUDA"
+CMBLensingMuseInferenceExt = "MuseInference"
+CMBLensingPythonCallExt = "PythonCall"
+CMBLensingPythonPlotExt = "PythonPlot"
+
 [compat]
 AbstractFFTs = "0.5, 1"
 Adapt = "1.0.1, 2, 3"
-CUDA = "3.4"
-CUDAKernels = "0.3.3, 0.4"
+CUDA = "3.4, 4"
 ChainRules = "1.5"
 CodecZlib = "0.7"
 Combinatorics = "1"
@@ -95,21 +106,20 @@ Interpolations = "0.12.8, 0.13, 0.14"
 IterTools = "1.3"
 JLD2 = "0.4.30"
 KahanSummation = "0.1, 0.2"
-KernelAbstractions = "0.7.3, 0.8"
 Lazy = "0.13.2, 0.14, 0.15"
 Loess = "0.5"
 MacroTools = "0.5"
 Match = "1.1"
 Measurements = "2"
 Memoization = "0.2"
+MuseInference = "0.2.2"
 NFFT = "0.13.3"
 NamedTupleTools = "0.13"
 Optim = "1"
 PDMats = "0.11.5"
 PlotUtils = "1.3.2"
 Preferences = "1.2"
 ProgressMeter = "1.2"
-PyCall = "1.91.2"
 QuadGK = "2.3.1"
 RecipesBase = "1.3.2"
 Requires = "0.5, 1"
@@ -123,4 +133,12 @@ TimerOutputs = "0.5"
 Tullio = "0.3"
 UnPack = "1"
 Zygote = "0.6.21"
-julia = "1.7"
+julia = "1.8"
+
+[extras]
+CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
+CUDAKernels = "72cfdca4-0801-4ab0-bf6a-d52aa10adc57"
+KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
+MuseInference = "43b88160-90c7-4f71-933b-9d65205cd921"
+PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
+PythonPlot = "274fc56d-3b97-40fa-a1cd-1b4a50311bf9"

docker-compose.yml

@@ -34,6 +34,7 @@ services:
       - DOCS=${DOCS:-8000}
     volumes:
       - "./src:/home/cosmo/CMBLensing/src"
+      - "./ext:/home/cosmo/CMBLensing/ext"
       - "./docs:/home/cosmo/CMBLensing/docs"
       - "/home/cosmo/.julia"
     command: ["sh", "-c", "python3 -m http.server $$DOCS -d /home/cosmo/CMBLensing/docs/build & jupyter lab --ip=0.0.0.0 --no-browser --port $$PORT"]