Update plot.py

.github/workflows/pylint.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.12"]
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
@@ -17,6 +17,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install -r requirements.txt
         pip install pylint
     - name: Analysing the code with pylint
       run: |

.pylintrc

@@ -6,7 +6,7 @@
 extension-pkg-whitelist=
 
 # Specify a score threshold to be exceeded before program exits with error.
-fail-under=10.0
+fail-under=8.0
 
 # Add files or directories to the blacklist. They should be base names, not
 # paths.
@@ -60,86 +60,21 @@ confidence=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use "--disable=all --enable=classes
 # --disable=W".
-disable=print-statement,
-        parameter-unpacking,
-        unpacking-in-except,
-        old-raise-syntax,
-        backtick,
-        long-suffix,
-        old-ne-operator,
-        old-octal-literal,
-        import-star-module-level,
-        non-ascii-bytes-literal,
-        raw-checker-failed,
+disable=raw-checker-failed,
         bad-inline-option,
         locally-disabled,
         file-ignored,
         suppressed-message,
         useless-suppression,
         deprecated-pragma,
         use-symbolic-message-instead,
-        apply-builtin,
-        basestring-builtin,
-        buffer-builtin,
-        cmp-builtin,
-        coerce-builtin,
-        execfile-builtin,
-        file-builtin,
-        long-builtin,
-        raw_input-builtin,
-        reduce-builtin,
-        standarderror-builtin,
-        unicode-builtin,
-        xrange-builtin,
-        coerce-method,
-        delslice-method,
-        getslice-method,
-        setslice-method,
-        no-absolute-import,
-        old-division,
-        dict-iter-method,
-        dict-view-method,
-        next-method-called,
-        metaclass-assignment,
-        indexing-exception,
-        raising-string,
-        reload-builtin,
-        oct-method,
-        hex-method,
-        nonzero-method,
-        cmp-method,
-        input-builtin,
-        round-builtin,
-        intern-builtin,
-        unichr-builtin,
-        map-builtin-not-iterating,
-        zip-builtin-not-iterating,
-        range-builtin-not-iterating,
-        filter-builtin-not-iterating,
-        using-cmp-argument,
-        eq-without-hash,
-        div-method,
-        idiv-method,
-        rdiv-method,
-        exception-message-attribute,
-        invalid-str-codec,
-        sys-max-int,
-        bad-python3-import,
-        deprecated-string-function,
-        deprecated-str-translate-call,
-        deprecated-itertools-function,
-        deprecated-types-field,
-        next-method-defined,
-        dict-items-not-iterating,
-        dict-keys-not-iterating,
-        dict-values-not-iterating,
-        deprecated-operator-function,
-        deprecated-urllib-function,
-        xreadlines-attribute,
-        deprecated-sys-function,
-        exception-escape,
-        comprehension-escape
-
+        consider-using-f-string,
+        too-many-lines,
+        missing-function-docstring,
+        line-too-long,
+        trailing-whitespace,
+        duplicate-code,
+
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option
 # multiple time (only on the command line, not in the configuration file where

bootstrap.py

@@ -10,7 +10,7 @@
 __authors__ = ["Frédéric-Emmanuel Picca", "Jérôme Kieffer"]
 __contact__ = "[email protected]"
 __license__ = "MIT"
-__date__ = "03/03/2023"
+__date__ = "12/07/2024"
 
 import sys
 import os
@@ -23,6 +23,7 @@
 logging.basicConfig()
 logger = logging.getLogger("bootstrap")
 
+LIBPATH = ""
 
 def get_project_name(root_dir):
     """Retrieve project name by running python setup.py --name in root_dir.
@@ -116,14 +117,14 @@ def run_file(filename, argv):
         # Providing globals() as locals will force to feed the file into
         # globals() (for examples imports).
         # Without this any function call from the executed file loses imports
+        old_argv = sys.argv
+        sys.argv = full_args
+        logger.info("Patch the sys.argv: %s", sys.argv)
+        logger.info("Executing %s.main()", filename)
+        print("########### EXECFILE ###########")
+        module_globals = globals().copy()
+        module_globals['__file__'] = filename
         try:
-            old_argv = sys.argv
-            sys.argv = full_args
-            logger.info("Patch the sys.argv: %s", sys.argv)
-            logger.info("Executing %s.main()", filename)
-            print("########### EXECFILE ###########")
-            module_globals = globals().copy()
-            module_globals['__file__'] = filename
             execfile(filename, module_globals, module_globals)
         finally:
             sys.argv = old_argv
@@ -154,10 +155,10 @@ def run_entry_point(target_name, entry_point, argv):
     logger.info("Execute target %s (function %s from module %s) using importlib", target_name, function_name, module_name)
     full_args = [target_name]
     full_args.extend(argv)
+    old_argv = sys.argv
+    sys.argv = full_args
+    print("########### IMPORTLIB ###########")
     try:
-        old_argv = sys.argv
-        sys.argv = full_args
-        print("########### IMPORTLIB ###########")
         module = importlib.import_module(module_name)
         if hasattr(module, function_name):
             func = getattr(module, function_name)

src/freesas/align.py

@@ -429,6 +429,7 @@ def alignment_2models(self, save=True):
 
         :return dist: NSD after alignment
         """
+        dist = None
         models = self.models
         reference = models[0]
         molecule = models[1]

src/freesas/app/cormap.py

@@ -4,18 +4,18 @@
 __author__ = "Jérôme Kieffer"
 __license__ = "MIT"
 __copyright__ = "2015, ESRF"
-__date__ = "20/04/2020"
+__date__ = "12/07/2024"
 
 import os
 import logging
-import freesas
-from freesas.cormap import gof
-
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger("cormap")
-import numpy
+import glob
 from itertools import combinations
 from collections import namedtuple
+import numpy
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger("cormap")
+import freesas
+from freesas.cormap import gof
 from freesas.sasio import load_scattering_data
 from freesas.sas_argparser import SASParser
 
@@ -24,8 +24,7 @@
 import platform
 
 operatingSystem = platform.system()
-if operatingSystem == "Windows":
-    import glob
+
 
 
 def parse():

src/freesas/dnn.py

@@ -30,16 +30,18 @@ def linear(x):
 
 # Parse config.json
 def parse_config(config_path):
+    config = {}
     if isinstance(config_path, io.IOBase):
         config = json.load(config_path)
     elif os.path.exists(config_path):
         with open(config_path, 'r') as f:
             config = json.load(f)
-
+    else:
+        raise RuntimeError(f"config_path type {type(config_path)} not handled, got {config_path}")
     layer_dims = []
     activations = []
 
-    for layer in config['config']['layers']:
+    for layer in config.get('config',{}).get('layers', {}):
         if layer['class_name'] == 'InputLayer':
             layer_dims.append(layer['config']['batch_shape'][1])
         elif layer['class_name'] == 'Dense':

src/freesas/model.py

@@ -49,7 +49,7 @@ def __init__(self, molecule=None):
             self.header = ""  # header of the PDB file
             self.rfactor = None
         self.radius = 1.0  # unused at the moment
-        self.com = []
+        self.com = numpy.array([])
         self._fineness = None
         self._Rg = None
         self._Dmax = None

src/freesas/plot.py

@@ -85,7 +85,7 @@ def scatter_plot(
             ax.errorbar(
                 q,
                 I,
-                err,
+                numpy.maximum(0,err),
                 label=label_exp,
                 capsize=0,
                 color=exp_color,
@@ -100,7 +100,7 @@ def scatter_plot(
             ax.errorbar(
                 q,
                 I,
-                err,
+                numpy.maximum(0,err),
                 label=label_exp,
                 capsize=0,
                 color=exp_color,
@@ -210,7 +210,7 @@ def kratky_plot(
     xdata = q * Rg
     ydata = xdata * xdata * I / I0
     if err is not None:
-        dy = xdata * xdata * err / I0
+        dy = xdata * xdata * numpy.maximum(0,err) / abs(I0)
         dplot = ax.errorbar(
             xdata,
             ydata,
@@ -302,7 +302,7 @@ def guinier_plot(
     else:
         fig, ax = subplots(figsize=(12, 10))
     if err is not None:
-        dlogI = err[mask] / logI
+        dlogI = err[mask] / I[mask]
         ax.errorbar(
             q2,
             logI,