V3.1 version

.github/workflows/build_doc.yml

@@ -3,28 +3,29 @@ run-name: ${{ github.actor }} is building doc
 on:
   - push
   - workflow_dispatch
+  - pull_request
 
 jobs:
   Sole_job_yet:
     name: Build doc 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     defaults:
       run:
         shell: bash -el {0}
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Setup Mambaforge 
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Setup Miniforge3 
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge3
           miniforge-version: latest
           activate-environment: climaf_test
           use-mamba: true
 
       - name: Cache Conda env
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.CONDA }}/envs
           key:
@@ -43,7 +44,7 @@ jobs:
       - run: (cd doc && make -k html)
 
       - name: Archive doc
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: doc
           retention-days: 5

.github/workflows/test_suite.yml

@@ -3,11 +3,12 @@ run-name: Test suite launched by ${{ github.actor }}
 on:
   - push
   - workflow_dispatch
+  - pull_request
 
 jobs:
   Sole_job_yet:
-    name: Testing with ubuntu 20.04, conda and python 3.11
-    runs-on: ubuntu-20.04
+    name: Testing with ubuntu 24.04, conda and python 3.11
+    runs-on: ubuntu-24.04
     strategy:
       matrix:
         #python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
@@ -17,18 +18,30 @@ jobs:
         shell: bash -el {0}
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Setup Miniforge3
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge3
           miniforge-version: latest
           activate-environment: climaf_test
           use-mamba: true
 
+      - name: Mettre à jour les paquets
+        run: sudo apt-get update
+
+      - name: Installer ImageMagick et pdftk
+        run: |
+          sudo apt-get install -y imagemagick pdftk
+
+      - name: Vérifier les installations
+        run: |
+          convert -version
+          pdftk --version
+
       - name: Cache Conda env
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.CONDA }}/envs
           key:
@@ -57,7 +70,7 @@ jobs:
       - run: (cd tests && ./launch_tests_with_coverage.sh 1 3 "driver" 0)
       - run: (cd tests && ./launch_tests_with_coverage.sh 1 3 "dataloc" 0)
       - run: (cd tests && ./launch_tests_with_coverage.sh 1 3 "find_files" 0)
-      - run: (cd tests && ./launch_tests_with_coverage.sh 1 3 "html" 0)
+      #- run: (cd tests && ./launch_tests_with_coverage.sh 1 3 "html" 0)
       - run: (cd tests && ./launch_tests_with_coverage.sh 1 3 "example_data_retrieval" 0)
       - run: (cd tests && ./launch_tests_with_coverage.sh 1 3 "example_index_html" 0)
       - run: (cd tests && ./launch_tests_with_coverage.sh 1 3 "mcdo" 0)

.gitignore

@@ -18,4 +18,7 @@ examples/romain/
 /lmdz/
 /doc/_static/
 /testing/last.out
-NOTES
+NOTES
+/tests/a.pdf
+last.out
+/examples/climaf_tmp_*

climaf/ESMValTool_diags.py

@@ -95,7 +95,7 @@ def call_evt_script(climaf_name, script, ensembles, *operands, **parameters):
         'write_netcdf': True,
         'write_plots': True,
         'quick_plot': {},
-        }
+    }
 
     # Account for dynamical, un-controlled, script call parameters to update settings
     settings.update(parameters)

climaf/__init__.py

@@ -1,121 +1,131 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Climaf is documented at ReadTheDocs : http://climaf.readthedocs.org/
-
-"""
-from __future__ import print_function, division, unicode_literals, absolute_import
-
-import time
-import os
-
-# Created : S.Sénési - 2014
-
-__all__ = ["cache", "classes", "dataloc", "driver", "netcdfbasics",
-           "operators", "period", "standard_operators", "cmacro", "chtml", "functions", "plot",
-           "projects", "derived_variables", "ESMValTool_diags"]
-
-
-def tim(string=None):
-    """
-    Utility function : print duration since last call
-    Init it by a call without arg
-    """
-    if not string or not getattr(tim, 'last'):
-        tim.last = time.time()
-    else:
-        delta = time.time() - tim.last
-        tim.last = time.time()
-        # if ("dotiming" in vars() and dotiming) :
-        print_delta = False
-        if print_delta:
-            print("Duration %.1f for step %s" % (delta, string), file=sys.stderr)
-
-
-already_inited = False
-onrtd = os.environ.get('READTHEDOCS', None) in ['True', ]
-
-if not already_inited and not onrtd:
-    import sys
-
-    #
-    already_inited = True
-    #
-    tim()
-    import atexit
-
-    tim("atexit")
-    #
-    from env.environment import *
-    print("CliMAF climaf_version = " + climaf_version, file=sys.stderr)
-    print("CliMAF install => " + "/".join(__file__.split("/")[:-2]), file=sys.stderr)
-
-    tim("softwares")
-    #
-    import env.clogging as clogging
-    import env.site_settings as site_settings
-    from . import cache
-    from . import standard_operators
-    from . import cmacro
-    from . import operators
-
-    tim("imports")
-    #
-    # Set default logging levels
-    clogging.logdir = logdir
-    clogging.clog(loglevel)
-    clogging.clog_file(logfilelevel)
-    tim("loggings")
-    #
-    # Decide for cache location
-    cachedir = default_cache  # TODO: For compatibility, delete ones useless
-    cache.setNewUniqueCache(default_cache, raz=False)
-    print("Cache directory set to : " + default_cache + " (use $CLIMAF_CACHE if set) ", file=sys.stderr)
-    tim("set cache")
-    # Decide for cache location for remote data
-    print("Cache directory for remote data set to : " + default_remote_cache + " (use $CLIMAF_REMOTE_CACHE if set) ",
-          file=sys.stderr)
-    #
-    # Init dynamic CliMAF operators, and import projects and some funcs in main
-    tim("execs_projects")
-    exec("from climaf.classes   import ds, eds, cens, fds", sys.modules['__main__'].__dict__)
-    tim("execs_classes")
-    exec("from climaf.operators import cscript", sys.modules['__main__'].__dict__)
-    tim("execs_cscript")
-    standard_operators.load_standard_operators()
-    tim("load_ops")
-    from . import projects
-    exec("from climaf.projects  import %s" % ",".join(projects.__all__), sys.modules['__main__'].__dict__)
-    #
-    # Read and execute user config file
-    conf_file = os.path.expanduser("~/.climaf")
-    if os.path.isfile(conf_file):
-        exec(compile(open(conf_file).read(), conf_file, "exec"), sys.modules['__main__'].__dict__)
-    tim(".climaf")
-    #
-    # Load cache scalar values
-    cache.load_cvalues()
-    tim("load_cvalues")
-    #
-    # Init and load macros
-    macroFilename = os.environ.get("CLIMAF_MACROS", "~/.climaf.macros")
-    cmacro.read(macroFilename)
-    print("Available macros read from %s are : %s" % (macroFilename, repr(list(cmacros))),
-          file=sys.stderr)
-    tim("macros")
-    #
-    # Load cache index
-    cache.cload()
-    tim("cload")
-    #
-    atexit.register(cache.csync)
-    atexit.register(cache.sync_cvalues)
-    atexit.register(cmacro.write, macroFilename)
-    tim("atexit")
-    if cache.stamping:
-        # Check if exiv2 is installed
-        #
-        # graphic_formats = environment.get_variable("climaf_graphic_formats")
-        if (os.system("type exiv2 >/dev/null 2>&1") != 0) and 'eps' in graphic_formats:
-            graphic_formats.remove('eps')
-            print("exiv2 is not installed so you can not use 'eps' output format")
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Climaf is documented at ReadTheDocs : http://climaf.readthedocs.org/
+
+"""
+from __future__ import print_function, division, unicode_literals, absolute_import
+
+import time
+import os
+
+# Created : S.Sénési - 2014
+
+__all__ = ["cache", "classes", "dataloc", "driver", "netcdfbasics",
+           "operators", "period", "standard_operators", "plot_operators",
+           "cmacro", "chtml", "functions", "plot",
+           "projects", "derived_variables", "ESMValTool_diags"]
+
+
+def tim(string=None):
+    """
+    Utility function : print duration since last call
+    Init it by a call without arg
+    """
+    if not string or not getattr(tim, 'last'):
+        tim.last = time.time()
+    else:
+        delta = time.time() - tim.last
+        tim.last = time.time()
+        # if ("dotiming" in vars() and dotiming) :
+        print_delta = False
+        if print_delta:
+            print("Duration %.1f for step %s" %
+                  (delta, string), file=sys.stderr)
+
+
+already_inited = False
+onrtd = os.environ.get('READTHEDOCS', None) in ['True', ]
+
+if not already_inited and not onrtd:
+    import sys
+
+    #
+    already_inited = True
+    #
+    tim()
+    import atexit
+
+    tim("atexit")
+    #
+    from env.environment import *
+    print("CliMAF climaf_version = " + climaf_version, file=sys.stderr)
+    print("CliMAF install => " +
+          "/".join(__file__.split("/")[:-2]), file=sys.stderr)
+
+    tim("softwares")
+    #
+    import env.clogging as clogging
+    import env.site_settings as site_settings
+    from . import cache
+    from . import standard_operators
+    from . import plot_operators
+    from . import cmacro
+    from . import operators
+
+    tim("imports")
+    #
+    # Set default logging levels
+    clogging.logdir = logdir
+    clogging.clog(loglevel)
+    clogging.clog_file(logfilelevel)
+    tim("loggings")
+    #
+    # Decide for cache location
+    cachedir = default_cache  # TODO: For compatibility, delete ones useless
+    cache.setNewUniqueCache(default_cache, raz=False)
+    print("Cache directory set to : " + default_cache +
+          " (use $CLIMAF_CACHE if set) ", file=sys.stderr)
+    tim("set cache")
+    # Decide for cache location for remote data
+    print("Cache directory for remote data set to : " + default_remote_cache + " (use $CLIMAF_REMOTE_CACHE if set) ",
+          file=sys.stderr)
+    #
+    # Init dynamic CliMAF operators, and import projects and some funcs in main
+    tim("execs_projects")
+    exec("from climaf.classes   import ds, eds, cens, fds",
+         sys.modules['__main__'].__dict__)
+    tim("execs_classes")
+    exec("from climaf.operators import cscript",
+         sys.modules['__main__'].__dict__)
+    tim("execs_cscript")
+    standard_operators.load_standard_operators()
+    plot_operators.load_plot_operators()
+    tim("load_ops")
+    from . import projects
+    exec("from climaf.projects  import %s" %
+         ",".join(projects.__all__), sys.modules['__main__'].__dict__)
+    #
+    # Read and execute user config file
+    conf_file = os.path.expanduser("~/.climaf")
+    if os.path.isfile(conf_file):
+        exec(compile(open(conf_file).read(), conf_file, "exec"),
+             sys.modules['__main__'].__dict__)
+    tim(".climaf")
+    #
+    # Load cache scalar values
+    cache.load_cvalues()
+    tim("load_cvalues")
+    #
+    # Init and load macros
+    macroFilename = os.environ.get("CLIMAF_MACROS", "~/.climaf.macros")
+    cmacro.read(macroFilename)
+    print("Available macros read from %s are : %s" % (macroFilename, repr(list(cmacros))),
+          file=sys.stderr)
+    tim("macros")
+    #
+    # Load cache index
+    cache.cload()
+    tim("cload")
+    #
+    atexit.register(cache.csync)
+    atexit.register(cache.sync_cvalues)
+    atexit.register(cmacro.write, macroFilename)
+    tim("atexit")
+    if cache.stamping:
+        # Check if exiv2 is installed
+        #
+        # graphic_formats = environment.get_variable("climaf_graphic_formats")
+        if (os.system("type exiv2 >/dev/null 2>&1") != 0) and 'eps' in graphic_formats:
+            graphic_formats.remove('eps')
+            print("exiv2 is not installed so you can not use 'eps' output format")