Python Logger/C++ Debug Mechanism Addition and Journal removal

.github/workflows/actions.yml

@@ -29,7 +29,7 @@ jobs:
     - name: Install histogram
       run: python -m pip install -e .
     - name: Run tests
-      run: xvfb-run --server-args="-screen 0 1920x1080x24" -a python -m pytest --cov --cov-report=xml --cov-report=term --cov-config=.coveragerc
+      run:  python -m pytest --log-cli-level=INFO  --cov=src --cov-report=xml --cov-report=term
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v4
       with:

.travis.yml

@@ -26,7 +26,7 @@ install:
   - conda update conda
   - conda config --add channels conda-forge
   - conda config --add channels mcvine
-  - conda create -n testenv python=$TRAVIS_PYTHON_VERSION anaconda-client future pytest gxx_linux-64=7 cmake danse.ins journal pyre h5py matplotlib
+  - conda create -n testenv python=$TRAVIS_PYTHON_VERSION anaconda-client future pytest gxx_linux-64=7 cmake danse.ins pyre h5py matplotlib
   - source activate testenv
   - conda config --set anaconda_upload no
   - export SRC=$PWD

CMakeLists.txt

@@ -30,13 +30,13 @@ set (PKGCLOUD_REPO "ins")
 # set(DOCKER_PKGING_DEB_DIST_NAME "ubuntu")
 # set(DOCKER_PKGING_DEB_DIST_VERSION "12.04")
 # dependencies
-set (DOCKER_PKGING_DEPS_DEB "python-numpy danse.ins journal pyre")
-set (DOCKER_PKGING_DEPS_RPM "numpy danse.ins journal pyre")
+set (DOCKER_PKGING_DEPS_DEB "python-numpy danse.ins pyre")
+set (DOCKER_PKGING_DEPS_RPM "numpy danse.ins pyre")
 set (DOCKER_PKGING_TEST_SRPM ". /opt/danse/bin/setup-danse.sh && python -c 'import histogram as p; print p'")
 set (DOCKER_PKGING_TEST_RPM ${DOCKER_PKGING_TEST_SRPM})
 set (DOCKER_PKGING_TEST_DEB ${DOCKER_PKGING_TEST_SRPM})
-set (CONDA_PKGING_BUILD_DEPS "python numpy journal")
-set (CONDA_PKGING_RUN_DEPS "python numpy danse.ins journal pyre h5py")
+set (CONDA_PKGING_BUILD_DEPS "python numpy")
+set (CONDA_PKGING_RUN_DEPS "python numpy danse.ins pyre h5py")
 
 # variables
 set (PYBINDING_NAME "${PROJECT_NAME}module")

conda.recipe/meta.yaml

@@ -36,8 +36,7 @@ requirements:
     - versioningit
   run:
     - numpy
-    - pyre
-    - journal
+    - pyre=0.8.3
 
 test:
   imports:

environment.yml

@@ -13,15 +13,15 @@ dependencies:
   - coverage
   - cmake
   - gxx_linux-64
-  - numpy >= 1.20.3,< 2.0
-  - python >=3.8
+  - numpy == 1.26.4
+  - python >=3.10
   - pyre == 0.8.3
-  - journal==0.8.4
   - matplotlib
   - h5py
   - pre-commit
   - pytest
   - pytest-cov
+  - pytest-xvfb
   - python-build
   - sphinx
   - sphinx-rtd-theme

lib/CMakeLists.txt

@@ -47,8 +47,6 @@ add_definitions(-DUSE_DANSE_NAMESPACE )
 
 # include python headers
 include_directories( ${PYTHON_INCLUDE_DIRS} )
-# assume journal is already deployed at the same deployment prefix
-# where we are going to deploy histogram
 include_directories( ${DEPLOYMENT_PREFIX}/include )
 
 # export headers from this project

lib/Histogrammer.h

@@ -16,7 +16,6 @@
 #define H_HISTOGRAM_HISTOGRAMMER
 
 #include "OutOfBound.h"
-#include "journal/warning.h"
 
 HISTOGRAM_NAMESPACE_START
 
@@ -50,10 +49,7 @@ HISTOGRAM_NAMESPACE_START
       IDataType i = m_e2x( e, m_x );
       if (m_fx.isOutofbound(m_x)) {
 #ifdef DEBUG
-	journal::warning_t warning("Histogrammer1");
-	warning << journal::at(__HERE__)
-		<< "OutOfBound: " << m_x
-		<< journal::endl;
+  printf("Warning Histogrammer1 %s:%d\n", __FILE__, __LINE__);
 #endif
 	return;
       }
@@ -65,10 +61,7 @@ HISTOGRAM_NAMESPACE_START
       }
       catch (OutOfBound & e) {
 #ifdef DEBUG
-	journal::warning_t warning("Histogrammer1");
-	warning << journal::at(__HERE__)
-		<< e.what()
-		<< journal::endl;
+  printf("Warning Histogrammer1 %s:%d\n", __FILE__, __LINE__);
 #endif
       }
     }
@@ -117,10 +110,7 @@ HISTOGRAM_NAMESPACE_START
       IDataType i = m_e2xy( e, m_x, m_y );
       if (m_fxy.isOutofbound(m_x, m_y)) {
 #ifdef DEBUG
-	journal::warning_t warning("Histogrammer2");
-	warning << journal::at(__HERE__)
-		<< "OutOfBound: " << m_x << ", " << m_y
-		<< journal::endl;
+  printf("Warning Histogrammer1 %s:%d\n", __FILE__, __LINE__);
 #endif
 	return;
       }
@@ -132,10 +122,7 @@ HISTOGRAM_NAMESPACE_START
       }
       catch (OutOfBound & e) {
 #ifdef DEBUG
-	journal::warning_t warning("Histogrammer2");
-	warning << journal::at(__HERE__)
-		<< e.what()
-		<< journal::endl;
+  printf("Warning Histogrammer1 %s:%d\n", __FILE__, __LINE__);
 #endif
       }
     }
@@ -186,10 +173,7 @@ HISTOGRAM_NAMESPACE_START
       IDataType i = m_e2xxxx( e, m_x1, m_x2, m_x3, m_x4 );
       if (m_fxxxx.isOutofbound( m_x1, m_x2, m_x3, m_x4 )) {
 #ifdef DEBUG
-	journal::warning_t warning("Histogrammer4");
-	warning << journal::at(__HERE__)
-		<< "OutOfBound: " << m_x1 << ", " << m_x2 << ", " << m_x3 << ", " << m_x4
-		<< journal::endl;
+  printf("Warning Histogrammer1 %s:%d\n", __FILE__, __LINE__);
 #endif
 	return;
       }
@@ -201,10 +185,7 @@ HISTOGRAM_NAMESPACE_START
       }
       catch (OutOfBound & e) {
 #ifdef DEBUG
-	journal::warning_t warning("Histogrammer4");
-	warning << journal::at(__HERE__)
-		<< e.what()
-		<< journal::endl;
+  printf("Warning Histogrammer1 %s:%d\n", __FILE__, __LINE__);
 #endif
       }
     }

lib/NdArray.h

@@ -18,9 +18,6 @@
 #include <vector>
 #include "OutOfBound.h"
 
-#include "journal/debug.h"
-
-
 HISTOGRAM_NAMESPACE_START
 
   /// Multiple dimensional array.
@@ -70,24 +67,17 @@ HISTOGRAM_NAMESPACE_START
     {
       m_size1D = 1;
 #ifdef DEBUG
-      journal::debug_t debug("NdArray");
-      debug << journal::at(__HERE__)
-	    << "dimension: " << dimension() << journal::endl
-	    << "shape: " ;
+  printf("Warning NdArray %s:%d\n", __FILE__, __LINE__);
 #endif
 
       for (unsigned int i=0; i<NDimension; i++) {
 	m_shape[i] = shape[i];
 	m_size1D *= shape[i];
 #ifdef DEBUG
-      debug
-	<< shape[i] << ", ";
-#endif
-      }
-#ifdef DEBUG
-      debug << journal::endl;
+  printf("Warning NdArray %s:%d -- shape[%d] = %d\n", __FILE__, __LINE__, i, shape[i]);
 #endif
     }
+  }
 
     /// dtor.
     ~NdArray() { }

lib/README

@@ -1,5 +1,5 @@
 c++ library for histogram-related stuff
-This library depends on pyre journal.
+This library used to depend on pyre journal. (It has currently been removed.)
 The distributed histogram python package does not need
 to contain this c++ library.
 

lib/events2histogram.h

@@ -21,9 +21,6 @@
 #include "_macros.h"
 
 
-#ifdef DEBUG
-#include "journal/debug.h"
-#endif
 
 
 HISTOGRAM_NAMESPACE_START
@@ -35,7 +32,7 @@ HISTOGRAM_NAMESPACE_START
    histogrammer_t & her )
   {
 #ifdef DEBUG
-    journal::debug_t debug("events2histogram");
+    printf("Warning events2histogram %s:%d \n", __FILE__, __LINE__);
 #endif
     std::for_each(events_begin, events_end, her);
   }

pyproject.toml

@@ -2,9 +2,9 @@
 name = "histogram-dev"
 description = "The histogram python package provides a simple yet fundamental data structure for scientific computing histogram"
 dynamic = ["version"]
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 dependencies = [
-  "numpy >= 1.20.3,< 2.0",
+  "numpy == 1.26.4"
 ]
 license = { text = "MIT" }
 keywords = ["neutrons", "histogram", "python"]
@@ -56,7 +56,8 @@ histogram-cli = "histogram.Histogram:main"
 
 # pytest.ini
 [tool.pytest.ini_options]
-
+log_cli = true
+log_file_format = "%(asctime)s [%(levelname)8s] (%(path)s:%(lineno)s) %(message)s"
 norecursedirs = [".svn","_build"] # ignore tests in ndarray due to missing stdVector module not found
 
 testpaths =[

rpm.spec.in

@@ -12,7 +12,6 @@ BuildRequires:  gcc-c++
 BuildRequires:	cmake > 2.6
 BuildRequires:	make
 BuildRequires:  python-devel
-BuildRequires:  journal
 
 Requires: python
 Requires: python-h5py

src/histogram/AxisMapperCreater.py

@@ -2,9 +2,9 @@
 # Jiao Lin Copyright (c) 2005 All rights reserved
 
 
-import journal
+import logging
 
-debug = journal.debug("ins.histogram.AxisMapperCreater")
+logger = logging.getLogger("Histogram")
 
 
 from .EvenlyContinuousAxisMapper import EvenlyContinuousAxisMapper

src/histogram/DatasetBase.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 # Timothy M. Kelley Copyright (c) 2005 All rights reserved
 
-import journal
+import logging
 
-debug = journal.debug("histogram.DatasetBase")
+logger = logging.getLogger("Histogram")
 
 
 msg = "class {0!s} must override {1!s}"

src/histogram/DatasetContainer.py

@@ -1,9 +1,8 @@
 #!/usr/bin/env python
 # Timothy M. Kelley Copyright (c) 2005 All rights reserved
+import logging
 
-import journal
-
-debug = journal.debug("histogram")
+logger = logging.getLogger("Histogram")
 
 
 class DatasetContainer(object):
@@ -22,7 +21,7 @@ def addDataset(self, name, id, dataset):
         # 1. store by name
         if name not in self._byNames:
             self._byNames[name] = dataset
-            debug.log("{0!s} added dataset {1!s}".format(self, name))
+            logger.debug("{0!s} added dataset {1!s}".format(self, name))
         else:
             msg = "container already has dataset named {0!s}".format(name)
             raise ValueError(msg)
@@ -79,7 +78,7 @@ def replaceDataset(self, name=None, dataset=None, id=None):
         name = name or self._id2name[id]
         id = id or self._name2id[name]
 
-        debug.log("{0!s} replaced dataset {1!s} (id={2!s})".format(self, name, id))
+        logger.debug("{0!s} replaced dataset {1!s} (id={2!s})".format(self, name, id))
 
         self._byNames[name] = dataset
         self._byIds[id] = [name, dataset]

src/histogram/Histogram.py

@@ -7,13 +7,13 @@
 ## in histogram.__init__ package to create histogram.
 
 
-import journal
 from functools import reduce
 
-debug = journal.debug("ins.histogram.Histogram")
-
 import operator
 from .DictAttributeCont import AttributeCont
+import logging
+
+logger = logging.getLogger("Histogram")
 
 
 class Histogram(AttributeCont):
@@ -301,7 +301,7 @@ def __setitem__(self, indexes_or_slice, v):
             if rhs is not None:
                 lhs[indexSlices] = rhs
             else:
-                debug.log("indefinite behavior: setting to None")
+                logger.debug("indefinite behavior: setting to None")
             continue
 
         return self[indexes_or_slice]
@@ -763,7 +763,7 @@ def size(self):
 
     def typeCode(self):
         """type code"""
-        debug.log(
+        logger.debug(
             "Histogram %s: typecode = %s" % (self.getAttribute("name"), self._typeCode)
         )
         return self._typeCode

src/histogram/NdArrayDataset.py

@@ -2,9 +2,9 @@
 # Jiao Lin Copyright (c) 2006 All rights reserved
 
 from .DatasetBase import DatasetBase
-import journal
+import logging
 
-debug = journal.debug("NdArrayDataset")
+logger = logging.getLogger("Histogram")
 
 
 class Dataset(DatasetBase):
@@ -34,8 +34,6 @@ def __init__(
         attributes = attributes or {}
         attributeCont = AttributeCont(dict(attributes))
 
-        # debug.log("storage = %s" % str(storage))
-
         if shape == [] and storage is not None:
             shape = storage.shape()
         if shape != [] and storage is not None:
@@ -48,8 +46,6 @@ def __init__(
         shape = list(shape)
         _checkShape(shape)
 
-        # debug.log("shape = %s" % (storage.shape(),))
-
         DatasetBase.__init__(self, name, unit, attributeCont, shape, storage)
         return
 
@@ -442,7 +438,7 @@ def isDataset(ds):
 
 def isCompatibleDataset(a, b):
     if not isinstance(a, DatasetBase) or not isinstance(b, DatasetBase):
-        debug.log(
+        logger.debug(
             "either %s or %s is not a dataset"
             % (
                 a.__class__.__name__,
@@ -452,7 +448,7 @@ def isCompatibleDataset(a, b):
         return False
 
     if a.shape() != b.shape():
-        debug.log("incompatible shape: %s, %s" % (a.shape(), b.shape()))
+        logger.debug("incompatible shape: %s, %s" % (a.shape(), b.shape()))
         return False
 
     return True
@@ -464,7 +460,7 @@ def isUnitCompatibleDataset(a, b):
     try:
         a.unit() + b.unit()
     except:
-        debug.log("incompatible units: %s, %s" % (a.unit(), b.unit()))
+        logger.debug("incompatible units: %s, %s" % (a.unit(), b.unit()))
         return False
     return True