Merge pull request #380 from threeML/root6-compatibility

Root6 compatibility
threeML · Oct 22, 2020 · 9e0d3da · 9e0d3da
2 parents a61cbe6 + 2a97a35
commit 9e0d3da
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Showing 13 changed files with 97 additions and 91 deletions.
diff --git a/build_local.sh b/build_local.sh
@@ -43,10 +43,10 @@ USE_LOCAL=false
 
 # Environment
 libgfortranver="3.0"
-NUMPYVER=1.15
+#NUMPYVER=1.15
 MATPLOTLIBVER=2
 UPDATE_CONDA=false
-XSPECVER="6.22.1"
+XSPECVER="6.25"
 xspec_channel=xspecmodels
 
 if [[ ${TRAVIS_OS_NAME} == "linux" ]];
@@ -56,10 +56,9 @@ then
 else  # osx
     miniconda_os=MacOSX
     compilers="clang_osx-64 clangxx_osx-64 gfortran_osx-64"
-
     # On macOS we also need the conda libx11 libraries used to build xspec
     # We also need to pin down ncurses, for now only on macos.
-    xorg="xorg-libx11 ncurses=5"
+    xorg="xorg-libx11"
 fi
 
 # Get the version in the __version__ environment variable
@@ -74,7 +73,7 @@ echo "Python version: ${TRAVIS_PYTHON_VERSION}"
 echo "Use local is: ${USE_LOCAL}"
 
 if ${USE_LOCAL}; then
-    conda config --remove channels ${xspec_channel}
+    #conda config --remove channels ${xspec_channel}
     use_local="--use-local"
 else
     conda config --add channels ${xspec_channel}
@@ -94,9 +93,10 @@ if [ -n "${XSPECVER}" ];
 fi
 
 if [[ ${TRAVIS_PYTHON_VERSION} == 2.7 ]]; then
-    PKG="pytest<4 openblas-devel=0.3.6 tk=8.5.19 astroquery=0.3.10 ipopt<3.13 pygmo=2.11.4 emcee>=3 pandas>=0.23"
+    #PKG="pytest<4 openblas-devel=0.3.6 tk=8.5.19 astroquery=0.3.10 ipopt<3.13 pygmo=2.11.4 emcee>=3 pandas>=0.23 krb5=1.14.6"
+    PKG="pytest<4 astroquery=0.3.10 pygmo=2.11.4 emcee>=3 pandas>=0.23 ipopt<3.13 pyyaml"
 else
-    PKG="pytest pandas>=0.23 ultranest interpolation>=2.1.5"
+    PKG="pytest>=3.6 pandas>=0.23 ultranest interpolation>=2.1.5"
 fi
 
 echo "dependencies: ${MATPLOTLIB} ${NUMPY} ${XSPEC}"
@@ -112,13 +112,13 @@ conda config --add channels defaults
 
 conda config --add channels threeml
 
-conda config --add channels conda-forge/label/cf201901
+#conda config --add channels conda-forge/label/cf201901
 
 conda config --add channels conda-forge
 
 # Create test environment
 echo "Create test environment..."
-conda create --yes --name $ENVNAME -c conda-forge ${use_local} python=$TRAVIS_PYTHON_VERSION ${PKG} codecov pytest-cov git ${MATPLOTLIB} ${NUMPY} ${XSPEC} astropy ${compilers} scipy krb5=1.14.6
+conda create --yes --name $ENVNAME -c conda-forge ${use_local} python=$TRAVIS_PYTHON_VERSION ${PKG} codecov pytest-cov git ${MATPLOTLIB} ${NUMPY} ${XSPEC} astropy ${compilers} scipy
 
 #openblas-devel=0.3.6 tk=8.5.19 astroquery=0.3.10 pygmo=2.11.4 "pytest<4"
 #libgfortran=${libgfortranver}
@@ -128,7 +128,7 @@ conda create --yes --name $ENVNAME -c conda-forge ${use_local} python=$TRAVIS_PY
 echo "Activate test environment..."
 
 source $CONDA_PREFIX/etc/profile.d/conda.sh
-#source $HOME/work/fermi/miniconda3/etc/profile.d/conda.sh
+#source $HOME/work/miniconda3/etc/profile.d/conda.sh
 conda activate $ENVNAME
 
 # Build package

diff --git a/ci/build_and_test.sh b/ci/build_and_test.sh
@@ -24,7 +24,7 @@ else  # osx
 
     # On macOS we also need the conda libx11 libraries used to build xspec
     # We also need to pin down ncurses, for now only on macos.
-    xorg="xorg-libx11 ncurses=5"
+    xorg="xorg-libx11"
 fi
 
 
@@ -39,10 +39,10 @@ echo "HOME= ${HOME}"
 echo "Building ${PKG_VERSION} ..."
 echo "Python version: ${TRAVIS_PYTHON_VERSION}"
 
-libgfortranver="3.0"
-NUMPYVER=1.15
+#libgfortranver="3.0"
+#NUMPYVER=1.15
 MATPLOTLIBVER=2
-XSPECVER="6.22.1"
+XSPECVER="6.25"
 xspec_channel=xspecmodels
 
 echo "Building ${PKG_VERSION} ..."
@@ -60,9 +60,9 @@ if [ -n "${XSPECVER}" ];
 fi
 
 if [[ ${TRAVIS_PYTHON_VERSION} == 2.7 ]]; then
-    PKG="pytest<4 openblas-devel=0.3.6 tk=8.5.19 astroquery=0.3.10 ipopt<3.13 pygmo=2.11.4 emcee>=3 pandas>=0.23"
+    PKG="pytest<4 astroquery=0.3.10 pygmo=2.11.4 emcee>=3 pandas>=0.23 ipopt<3.13 pyyaml"
 else
-    PKG="pytest pandas>=0.23 ultranest interpolation>=2.1.5"
+    PKG="pytest>=3.6 pandas>=0.23 ultranest interpolation>=2.1.5"
 fi
 
 echo "dependencies: ${MATPLOTLIB} ${NUMPY}  ${XSPEC}"
@@ -78,12 +78,12 @@ conda config --add channels defaults
 
 conda config --add channels threeml
 
-conda config --add channels conda-forge/label/cf201901
+#conda config --add channels conda-forge/label/cf201901
 
 conda config --add channels conda-forge
 
 # Create test environment
-conda create --yes --name test_env -c conda-forge python=$TRAVIS_PYTHON_VERSION ${PKG} codecov pytest-cov git ${MATPLOTLIB} ${NUMPY} ${XSPEC} astropy ${compilers} scipy krb5=1.14.6
+conda create --yes --name test_env -c conda-forge python=$TRAVIS_PYTHON_VERSION ${PKG} codecov pytest-cov git ${MATPLOTLIB} ${NUMPY} ${XSPEC} astropy ${compilers} scipy
 
 if [[ "$TRAVIS_OS_NAME" == "removeme" ]]; then
 

diff --git a/ci/cron_install_and_test.sh b/ci/cron_install_and_test.sh
@@ -22,34 +22,14 @@ elif  (( $TRAVIS_BUILD_NUMBER % 4 == 1 )); then
 # Testing with xspec and root
 elif  (( $TRAVIS_BUILD_NUMBER % 4 == 2 )); then
 
-    if [[ $TRAVIS_PYTHON_VERSION == "2.7" ]]; then
-
-        echo "Testing with xspec-modelsonly and root with python $TRAVIS_PYTHON_VERSION"
-        bash install_3ML.sh --batch --with-xspec --with-root --python $TRAVIS_PYTHON_VERSION
-
-    else
-
-        echo "Root5 is not available for python 3."
-        echo "Cannot test with xspec-modelsonly and root. Exiting."
-        exit 0
-
-    fi
+    echo "Testing with xspec-modelsonly and root with python $TRAVIS_PYTHON_VERSION"
+    bash install_3ML.sh --batch --with-xspec --with-root --python $TRAVIS_PYTHON_VERSION
 
 # Testing with Fermi software
 else
 
-    if [[ $TRAVIS_PYTHON_VERSION == "2.7" ]]; then
-
-        echo "Testing with xspec-modelsonly and Fermi software with python $TRAVIS_PYTHON_VERSION"
-        bash install_3ML.sh --batch --with-xspec --with-fermi --python $TRAVIS_PYTHON_VERSION
-
-    else
-
-        echo "Fermi tools are not available for python 3 yet."
-        echo "Cannot test with xspec-modelsonly and Fermi software. Exiting."
-        exit 0
-
-    fi
+    echo "Testing with xspec-modelsonly and Fermi software with python $TRAVIS_PYTHON_VERSION"
+    bash install_3ML.sh --batch --with-xspec --with-fermi --python $TRAVIS_PYTHON_VERSION
 
 fi
 

diff --git a/conda-dist/recipes/threeml/meta.yaml b/conda-dist/recipes/threeml/meta.yaml
@@ -22,17 +22,16 @@ requirements:
     - python
     #- setuptools
     #- toolchain
-    - numpy>=1.15,<1.16 # [py2k]
-    - numpy>=1.15 # [py3k]
+    - numpy>=1.15
     #- scipy >=0.18
     - emcee>=3
     #- astropy >=1.0.3
     #- matplotlib
     - uncertainties
-    - pyyaml==3.13
+    - pyyaml>=5.1
     - dill
     - iminuit>=1.2
-    - astromodels
+    - astromodels>=2
     - astroquery<0.4 # [py2k]
     - astroquery # [py3k]
     - corner>=1.0.2
@@ -43,32 +42,30 @@ requirements:
     - pymultinest
     - ultranest # [py3k]
     - dynesty>=1
-    - pygmo>=2.4,<=2.11.4 # [py2k]
-    - pygmo>=2.4 # [py3k]
+    #- pygmo>=2.4,<=2.11.4 # [py2k]
+    - pygmo>=2.4
     - ipywidgets
     - numba
     #- ipython
     - ipyparallel
     - py
-    - tk==8.5.19 # [py2k]
+    #- tk==8.5.19 # [py2k]
     - ipopt<3.13 # [py2k]
     - numdifftools
     - interpolation>=2.1.5 # [py3k]
 
-
   run:
     - python
-    - numpy>=1.15,<1.16 # [py2k]
     - numpy>=1.15 # [py3k]
     - scipy>=0.18
     - emcee>=3
     - astropy>=1.0.3
     - matplotlib
     - uncertainties
-    - pyyaml==3.13
+    - pyyaml>=5.1
     - dill
     - iminuit>=1.2
-    - astromodels
+    - astromodels>=2
     - astroquery<0.4 # [py2k]
     - astroquery # [py3k]
     - corner>=1.0.2
@@ -78,8 +75,8 @@ requirements:
     - pymultinest
     - ultranest # [py3k]
     - dynesty>=1
-    - pygmo>=2.4,<=2.11.4 # [py2k]
-    - pygmo>=2.4 # [py3k]
+    #- pygmo>=2.4,<=2.11.4 # [py2k]
+    - pygmo>=2.4
     - ipywidgets
     - ipython
     - ipyparallel

diff --git a/install_3ML.sh b/install_3ML.sh
@@ -264,35 +264,32 @@ conda config --add channels defaults
 
 conda config --add channels threeml
 
-conda config --add channels conda-forge/label/cf201901
-
 conda config --add channels conda-forge
 
-if [[ ${PYTHON_VERSION} == "2.7" ]]; then
-    conda config --add channels conda-forge/label/cf201901
-fi
-
-PACKAGES_TO_INSTALL="astromodels threeml"
+PACKAGES_TO_INSTALL="astromodels>=2 threeml"
 
 if [[ "${INSTALL_XSPEC}" == "yes" ]]; then
 
-    PACKAGES_TO_INSTALL="${PACKAGES_TO_INSTALL} xspec-modelsonly=6.22.1"
+    PACKAGES_TO_INSTALL="${PACKAGES_TO_INSTALL} xspec-modelsonly=6.25"
     conda config --add channels xspecmodels
 
 fi
 
 if [[ "${INSTALL_ROOT}" == "yes" ]]; then
 
-    PACKAGES_TO_INSTALL="${PACKAGES_TO_INSTALL} root5"
+    PACKAGES_TO_INSTALL="${PACKAGES_TO_INSTALL} root"
 
 fi
 
 if [[ "${INSTALL_FERMI}" == "yes" ]]; then
 
-    PACKAGES_TO_INSTALL="${PACKAGES_TO_INSTALL} fermitools fermipy"
-
-    #conda config --add channels conda-forge/label/cf201901
-    conda config --add channels fermi
+    if [[ $PYTHON_VERSION == "2.7" ]]; then
+        conda config --add channels fermi/label/master
+        PACKAGES_TO_INSTALL="${PACKAGES_TO_INSTALL} clhep=2.4.1.0"
+    else
+        conda config --add channels fermi
+    fi
+    PACKAGES_TO_INSTALL="${PACKAGES_TO_INSTALL} fermitools"
 
 fi
 
@@ -483,14 +480,7 @@ EOM
 conda activate ${ENV_NAME}
 
 # Fix needed to solve the "readinto" AttributeError due to older future package
-conda install --yes -c conda-forge future
-
-# Workaround needed to meet the requirement on ccfits on linux systems
-if [[ "$os_guessed" == "linux" ]] && [[ "${INSTALL_XSPEC}" == "yes" ]]; then
-    conda install --yes -c conda-forge ccfits=2.5
-elif [[ "$os_guessed" == "osx" ]] && [[ "${INSTALL_XSPEC}" == "yes" ]]; then
-    conda install --yes -c conda-forge/label/cf201901 ccfits=2.5
-fi
+#conda install --yes -c conda-forge future
 
 mv activate.csh $CONDA_PREFIX/bin
 mv deactivate.csh $CONDA_PREFIX/bin

diff --git a/setup.cfg b/setup.cfg
@@ -37,7 +37,7 @@ install_requires =
     astropy>=1.3.3
     matplotlib
     uncertainties
-    pyyaml==3.13
+    pyyaml>=5.1
     dill
     iminuit>=1.2
     astromodels

diff --git a/threeML/__init__.py b/threeML/__init__.py
@@ -17,6 +17,16 @@
 
     mpl.use("Agg")
 
+# Workaround to a CFITSIO issue
+try:
+    import ROOT
+except ImportError:
+    pass
+try:
+    import pyLikelihood
+except ImportError:
+    pass
+
 # Import version (this has to be placed before the import of serialization
 # since __version__ needs to be defined at that stage)
 from ._version import get_versions

diff --git a/threeML/analysis_results.py b/threeML/analysis_results.py
@@ -99,7 +99,7 @@ def _load_one_results(fits_extension):
 
     # Gather the optimized model
     serialized_model = _escape_back_yaml_from_fits(fits_extension.header.get("MODEL"))
-    model_dict = my_yaml.load(serialized_model)
+    model_dict = my_yaml.load(serialized_model, Loader=yaml.FullLoader)
 
     optimized_model = ModelParser(model_dict=model_dict).get_model()
 

diff --git a/threeML/config/config.py b/threeML/config/config.py
@@ -52,7 +52,7 @@ def __init__(self):
 
             try:
 
-                configuration = yaml.load(f)
+                configuration = yaml.load(f, Loader=yaml.FullLoader)
 
             except:
 
@@ -87,7 +87,7 @@ def __init__(self):
 
             with open(user_config_path) as f:
 
-                configuration = yaml.load(f)
+                configuration = yaml.load(f, Loader=yaml.FullLoader)
 
                 # Test if the local/configuration is ok
 

diff --git a/threeML/minimizer/ROOT_minimizer.py b/threeML/minimizer/ROOT_minimizer.py
@@ -35,22 +35,30 @@
     300: "Covariance matrix is not positive defined",
 }
 
-
-class FuncWrapper(ROOT.TPyMultiGenFunction):
-    def __init__(self, function, dimensions):
-
-        ROOT.TPyMultiGenFunction.__init__(self, self)
+#root_class = None
+#try:
+#    root_class = ROOT.TPyMultiGenFunction
+#except AttributeError:
+#    root_class = ROOT.Math.IMultiGenFunction
+
+class FuncWrapper(ROOT.Math.IMultiGenFunction):
+
+    def setup(self, function, dimensions):
         self.function = function
         self.dimensions = int(dimensions)
 
     def NDim(self):
         return self.dimensions
 
     def DoEval(self, args):
-
         new_args = [args[i] for i in range(self.dimensions)]
-
         return self.function(*new_args)
+
+    def Clone(self):
+        f = FuncWrapper()
+        f.setup(f.function, f.dimensions)
+        ROOT.SetOwnership(f, False)
+        return f
 
 
 class ROOTMinimizer(LocalMinimizer):
@@ -76,7 +84,8 @@ def _setup(self, user_setup_dict):
 
         # Setup the minimizer algorithm
 
-        self.functor = FuncWrapper(self.function, self.Npar)
+        self.functor = FuncWrapper()
+        self.functor.setup(self.function, self.Npar)
         self.minimizer = ROOT.Minuit2.Minuit2Minimizer("Minimize")
         self.minimizer.Clear()
         self.minimizer.SetMaxFunctionCalls(setup_dict["max_function_calls"])