require python<3.13

desihub · Dec 11, 2024 · ba861bd · ba861bd
2 parents 308383f + 48e25f5
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diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -16,7 +16,7 @@ jobs:
             fail-fast: true
             matrix:
                 os: [ubuntu-latest]
-                python-version: ['3.10', '3.11']
+                python-version: ['3.10', '3.11', '3.12']
         env:
             DESIUTIL_VERSION: 3.4.3
 
@@ -47,7 +47,7 @@ jobs:
             fail-fast: true
             matrix:
                 os: [ubuntu-latest]
-                python-version: ['3.10', '3.11']
+                python-version: ['3.10', '3.11', '3.12']
         env:
             DESIUTIL_VERSION: 3.4.3
 
@@ -80,7 +80,7 @@ jobs:
             fail-fast: false
             matrix:
                 os: [ubuntu-latest]
-                python-version: ['3.11']
+                python-version: ['3.12']
 
         steps:
             - name: Checkout code
@@ -103,7 +103,7 @@ jobs:
             fail-fast: false
             matrix:
                 os: [ubuntu-latest]
-                python-version: ['3.11']
+                python-version: ['3.12']
 
         steps:
             - name: Checkout code

diff --git a/doc/index.rst b/doc/index.rst
@@ -8,13 +8,16 @@ Welcome to the Documentation for FastSpecFit
 Overview
 --------
 
-``FastSpecFit`` is a stellar continuum and emission-line modeling code for `DESI
-<https://desi.lbl.gov>`_ which is optimized for speed and simplicity; it uses
-physically motivated stellar population synthesis and emission-line templates to
-jointly model the three-camera optical spectrophotometry from DESI and the
-ultraviolet through infrared broadband photometry (``fastspec``). Alternatively,
-it can be used to model just the broadband photometry (``fastphot``), although
-in either case DESI redshifts are required.
+``FastSpecFit`` is a stellar continuum and emission-line modeling code which is
+optimized for speed and simplicity; it uses physically motivated stellar
+population synthesis and emission-line templates to jointly model UV/optical
+spectrophotometry and ultraviolet through infrared broadband photometry
+(``fastspec``). Alternatively, it can be used to model just the broadband
+photometry (``fastphot``).
+
+``FastSpecFit`` currently only supports `DESI <https://desi.lbl.gov>`_
+spectrophotometric data, although contributions to develop the software for
+other instruments and surveys are more than welcome.
 
 Contents
 --------

diff --git a/docker/Containerfile b/docker/Containerfile
@@ -0,0 +1,103 @@
+FROM ubuntu:24.04
+
+RUN mkdir -p /src
+WORKDIR /src
+
+RUN apt-get -y clean && apt -y update && apt install -y apt-utils && apt -y upgrade && echo 1
+
+RUN DEBIAN_FRONTEND=noninteractive \
+    apt install -y --no-install-recommends \
+    build-essential \
+    gfortran \
+    wget \
+    git \
+    pkg-config \
+    libbz2-dev \ 
+    libgsl-dev \ 
+    libssl-dev \
+    libcfitsio-dev \
+    libcfitsio-bin \
+    # libhdf5 needed by h5py
+    libhdf5-dev \
+    # needed by mpich \
+    python3.12 \
+    python3.12-dev \
+    python3-pip \
+    # python3-mpi4py \
+    && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# python = python3
+RUN ln -s "$(which python3)" /usr/bin/python
+
+ARG mpich=4.1.1
+ARG mpich_prefix=mpich-$mpich
+
+ENV FFLAGS="-fallow-argument-mismatch" \
+    FCFLAGS="-fallow-argument-mismatch"
+
+RUN wget --no-check-certificate -nv https://www.mpich.org/static/downloads/$mpich/$mpich_prefix.tar.gz \
+    && tar xvzf $mpich_prefix.tar.gz \
+    && cd $mpich_prefix \
+    && ./configure \
+    && make -j 4 \
+    && make install \
+    && make clean \
+    && cd .. \
+    && rm -rf $mpich_prefix
+
+RUN /sbin/ldconfig
+
+RUN for x in \
+    wheel \
+    setuptools \
+    pytest \
+    numpy \
+    scipy \
+    astropy \
+    healpy \
+    fitsio \
+    numba \
+    intel-cmplr-lib-rt \
+    mpi4py \
+    seaborn \
+    matplotlib \
+    ipython \
+    ipykernel \
+    h5py \
+    ; do pip3 install --break-system-packages $x; done \
+    && rm -Rf /root/.cache/pip \
+    && echo 1
+
+ENV DESIUTIL_VERSION 3.4.3
+ENV DESIMODEL_VERSION 0.19.2
+ENV DESITARGET_VERSION 2.8.0
+ENV DESISPEC_VERSION 0.68.1
+ENV SPECLITE_VERSION v0.20
+ENV FASTSPECFIT_VERSION 3.1.0
+
+RUN pip3 install --break-system-packages git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil
+RUN pip3 install --break-system-packages git+https://github.com/desihub/desimodel.git@${DESIMODEL_VERSION}#egg=desimodel
+RUN pip3 install --break-system-packages git+https://github.com/desihub/desitarget.git@${DESITARGET_VERSION}#egg=desitarget
+RUN pip3 install --break-system-packages git+https://github.com/desihub/desispec.git@${DESISPEC_VERSION}#egg=desispec
+RUN pip3 install --break-system-packages git+https://github.com/desihub/speclite.git@${SPECLITE_VERSION}#egg=speclite
+RUN pip3 install --break-system-packages git+https://github.com/desihub/fastspecfit.git@${FASTSPECFIT_VERSION}#egg=fastspecfit && echo 1
+
+RUN mkdir /homedir && chmod 777 /homedir
+ENV HOME /homedir
+
+#ENV NUMBA_CACHE_DIR=/homedir/numba_cache
+#RUN chmod 777 /homedir/numba_cache
+
+# set prompt and default shell
+SHELL ["/bin/bash", "-c"]
+ENTRYPOINT ["/bin/bash", "-c"]
+CMD ["/bin/bash"]
+
+#RUN echo "export PS1='[container] \\u@\\h:\\w$ '" >> $HOME/.bashrc \
+#  # Create config files in $HOME
+#  && python -c "import astropy" \
+#  && python -c "import matplotlib.font_manager as fm; f = fm.FontManager()" \
+#  && ipython -c "print('hello')" \
+#  && echo 1
+
+LABEL Maintainer="John Moustakas [email protected]"
diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -1,9 +1,9 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04.1
 
 RUN mkdir -p /src
 WORKDIR /src
 
-RUN apt-get -y clean && apt -y update && apt install -y apt-utils && apt -y upgrade && echo 2
+RUN apt-get -y clean && apt -y update && apt install -y apt-utils && apt -y upgrade && echo 1
 
 RUN DEBIAN_FRONTEND=noninteractive \
     apt install -y --no-install-recommends \
@@ -19,7 +19,7 @@ RUN DEBIAN_FRONTEND=noninteractive \
     libcfitsio-bin \
     # libhdf5 needed by h5py
     libhdf5-dev \
-    # mpich \
+    # needed by mpich \
     python3-dev \
     python3-pip \
     # python3-mpi4py \
@@ -28,7 +28,7 @@ RUN DEBIAN_FRONTEND=noninteractive \
 # python = python3
 RUN ln -s "$(which python3)" /usr/bin/python
 
-ARG mpich=4.0.2
+ARG mpich=4.1.1
 ARG mpich_prefix=mpich-$mpich
 
 ENV FFLAGS="-fallow-argument-mismatch" \
@@ -56,6 +56,7 @@ RUN for x in \
     healpy \
     fitsio \
     numba \
+    intel-cmplr-lib-rt \
     mpi4py \
     seaborn \
     matplotlib \
@@ -64,28 +65,34 @@ RUN for x in \
     h5py \
     ; do pip3 install $x; done \
     && rm -Rf /root/.cache/pip \
-    && echo 2
+    && echo 1
 
-ENV DESIUTIL_VERSION 3.2.6
-ENV DESIMODEL_VERSION 0.18.0
-ENV DESITARGET_VERSION 2.6.0
-ENV DESISPEC_VERSION 0.57.0
-ENV SPECLITE_VERSION v0.16
-ENV FASTSPECFIT_VERSION 2.1.1
+RUN python -m pip install --index-url https://software.repos.intel.com/python/pypi \
+    --extra-index-url https://pypi.org/simple mkl_fft
+
+ENV DESIUTIL_VERSION 3.4.3
+ENV DESIMODEL_VERSION 0.19.2
+ENV DESITARGET_VERSION 2.8.0
+ENV DESISPEC_VERSION 0.68.1
+ENV SPECLITE_VERSION v0.20
+ENV FASTSPECFIT_VERSION main
 
 RUN pip3 install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil
 RUN pip3 install git+https://github.com/desihub/desimodel.git@${DESIMODEL_VERSION}#egg=desimodel
 RUN pip3 install git+https://github.com/desihub/desitarget.git@${DESITARGET_VERSION}#egg=desitarget
 RUN pip3 install git+https://github.com/desihub/desispec.git@${DESISPEC_VERSION}#egg=desispec
 RUN pip3 install git+https://github.com/desihub/speclite.git@${SPECLITE_VERSION}#egg=speclite
-RUN pip3 install git+https://github.com/desihub/fastspecfit.git@${FASTSPECFIT_VERSION}#egg=fastspecfit && echo 1.1
+RUN pip3 install git+https://github.com/desihub/fastspecfit.git@${FASTSPECFIT_VERSION}#egg=fastspecfit && echo 1
 
 ENV PYTHONPATH /src/fastspecfit/py
 ENV PATH /src/fastspecfit/bin:/opt/conda/bin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 
 RUN mkdir /homedir && chmod 777 /homedir
 ENV HOME /homedir
 
+ENV NUMBA_CACHE_DIR=/homedir/numba_cache
+RUN chmod 777 /homedir/numba_cache
+
 # set prompt and default shell
 SHELL ["/bin/bash", "-c"]
 ENTRYPOINT ["/bin/bash", "-c"]
@@ -96,15 +103,15 @@ RUN echo "export PS1='[container] \\u@\\h:\\w$ '" >> $HOME/.bashrc \
   && python -c "import astropy" \
   && python -c "import matplotlib.font_manager as fm; f = fm.FontManager()" \
   && ipython -c "print('hello')" \
-  # Download astropy site locations and USNO sky model
-  && python -c "from astropy.coordinates import EarthLocation; EarthLocation._get_site_registry(force_download=True)" \
-  && python -c "from astropy.coordinates import EarthLocation, SkyCoord, AltAz; from astropy.time import Time; print(EarthLocation.of_site('ctio')); print(SkyCoord(180.,-45.,unit='deg').transform_to(AltAz(obstime=Time(56806.0, format='mjd'), location=EarthLocation.of_site('ctio'))))" \
-  # Download astropy IERS leap-second list
-  && python -c "from astropy.time import Time; Time.now()" \
-  # Make astropy cache files readable!?!!
-  && chmod -R a+rwX $HOME/.astropy \
-  # Make ipython config files readable!?!!
-  && chmod -R a+rwX $HOME/.ipython \
-  && echo 2
+  ## Download astropy site locations and USNO sky model
+  #&& python -c "from astropy.coordinates import EarthLocation; EarthLocation._get_site_registry(force_download=True)" \
+  #&& python -c "from astropy.coordinates import EarthLocation, SkyCoord, AltAz; from astropy.time import Time; print(EarthLocation.of_site('ctio')); print(SkyCoord(180.,-45.,unit='deg').transform_to(AltAz(obstime=Time(56806.0, format='mjd'), location=EarthLocation.of_site('ctio'))))" \
+  ## Download astropy IERS leap-second list
+  #&& python -c "from astropy.time import Time; Time.now()" \
+  ## Make astropy cache files readable!?!!
+  #&& chmod -R a+rwX $HOME/.astropy \
+  ## Make ipython config files readable!?!!
+  #&& chmod -R a+rwX $HOME/.ipython \
+  && echo 1
 
 LABEL Maintainer="John Moustakas [email protected]"
diff --git a/docker/README.md b/docker/README.md
@@ -1,20 +1,47 @@
 Build a Docker container for fastspecfit.
 =========================================
 
+Using podman-hpc at NERSC
+-------------------------
+
+podman-hpc pull ubuntu:22.04
+
+First, build the container:
+```
+podman-hpc build -t desihub/fastspecfit:latest .
+```
+
+podman-hpc migrate desihub/fastspecfit:latest
+
+
+podman-hpc login docker.io
+podman-hpc push docker.io/desihub/fastspecfit:latest
+podman-hpc pull docker.io/desihub/fastspecfit:latest
+
+podman-hpc run --rm -it localhost/desihub/fastspecfit:latest /bin/bash
+
+
+
+Legacy Instructions
+-------------------
+
 Build a cross-platform docker container as documented [here](https://www.docker.com/blog/faster-multi-platform-builds-dockerfile-cross-compilation-guide), [here](https://blog.jaimyn.dev/how-to-build-multi-architecture-docker-images-on-an-m1-mac/), and [here](https://docs.nersc.gov/development/shifter/how-to-use/).
 
-First (but just once), create the builder instance:
+The very first time, create a builder instance with
+```
+docker buildx create --name FastSpecFit-build --node FastSpecFit --use
+```
+and then subsequently simply load that instance with
 ```
-docker buildx create --name mybuilder --use
+docker buildx use FastSpecFit-build
 ```
 
-Then, subsequently, to create a new (or the latest) version or tag:
+Then, subsequently, to create a new (or the latest) version or tag, do:
 ```
 export DOCKER_BUILDKIT=0
 export COMPOSE_DOCKER_CLI_BUILD=0
 
-docker buildx use mybuilder
-docker buildx build --platform linux/amd64,linux/arm64/v8 --push -t desihub/fastspecfit:2.1.1 .
+docker buildx build --platform linux/amd64,linux/arm64/v8 --push -t desihub/fastspecfit:3.1.2 .
 docker buildx build --platform linux/amd64,linux/arm64/v8 --push -t desihub/fastspecfit:latest .
 ```
 
@@ -25,8 +52,8 @@ docker run -it desihub/fastspecfit:latest
 ```
 or
 ```
-docker pull desihub/fastspecfit:2.1.1
-docker run -it desihub/fastspecfit:2.1.1
+docker pull desihub/fastspecfit:3.1.2
+docker run -it desihub/fastspecfit:3.1.2
 ```
 
 Or at NERSC:

diff --git a/py/fastspecfit/data/emlines.ecsv b/py/fastspecfit/data/emlines.ecsv
@@ -70,8 +70,8 @@ name restwave patch isbalmer ishelium isbroad isstrong nicename plotgroup
        nii_6584   6585.273     t   False  False False  True  H$\alpha$+[NII]-$\lambda\lambda$6548,84                      halpha_nii_6548_48
        sii_6716   6718.294     u   False  False False  True  [SII]-$\lambda\lambda$6716,31                                sii_6716_31
        sii_6731   6732.674     u   False  False False  True  [SII]-$\lambda\lambda$6716,31                                sii_6716_31
-     ariii_7135   7137.77      v   False  False False  False [ArIII]-$\lambda$7135                                        oii_7320_30
-       oii_7320   7321.94      v   False  False False  False [OII]-$\lambda\lambda$7320,30                                oii_7320_30
-       oii_7330   7332.21      v   False  False False  False [OII]-$\lambda\lambda$7320,30                                oii_7320_30
+     ariii_7135   7137.77      v   False  False False  False [ArIII]-$\lambda$7135+[OII]-$\lambda\lambda$7320,30          ariii_7135_oii_7320_30
+       oii_7320   7321.94      v   False  False False  False [ArIII]-$\lambda$7135+[OII]-$\lambda\lambda$7320,30          ariii_7135_oii_7320_30
+       oii_7330   7332.21      v   False  False False  False [ArIII]-$\lambda$7135+[OII]-$\lambda\lambda$7320,30          ariii_7135_oii_7320_30
       siii_9069   9071.1       w   False  False False  False [SIII]-$\lambda$9069                                         siii_9069
       siii_9532   9533.2       w   False  False False  False [SIII]-$\lambda$9532                                         siii_9532
diff --git a/py/fastspecfit/test/test_util.py b/py/fastspecfit/test/test_util.py
@@ -77,10 +77,10 @@ def test_stats():
     xgood, mask = sigmaclip(xx)
     assert(np.all(mask))
 
-    q1, q2 = quantile(xx, [0.1, 0.9])
+    q1, q2 = quantile(xx, np.asarray([0.1, 0.9]))
     assert(np.isclose(q1, 3.4) & np.isclose(q2, 30.6))
 
     with pytest.raises(ValueError):
-        quantile(xx, [10., 90.])
+        quantile(xx, np.asarray([10., 90.]))
 
     assert(np.isclose(median(xx), 17.))
diff --git a/pyproject.toml b/pyproject.toml
@@ -18,17 +18,17 @@ classifiers = [
     "Topic :: System :: Software Distribution",
 ]
 dependencies = [
-    "numpy<2.0",
-    "astropy>=5.0",
+    "numpy",
+    "astropy",
     "scipy",
     "healpy",
     "numba",
     "seaborn",
     "matplotlib",
     "fitsio",
-    "speclite>=0.20",
+    "speclite",
 ]
-requires-python = ">=3.9"
+requires-python = "<3.13"
 
 [project.optional-dependencies]
 test = [

diff --git a/requirements.txt b/requirements.txt
@@ -1,12 +1,12 @@
-numpy<2.0
-astropy>=5.0
+numpy
+astropy
 scipy
 healpy
 numba
 seaborn
 matplotlib
 fitsio
-speclite>=0.20
+speclite
 git+https://github.com/desihub/[email protected]
 git+https://github.com/desihub/[email protected]
 git+https://github.com/desihub/[email protected]