Fix bug with sep

.github/workflows/tests.yml

@@ -27,15 +27,6 @@ jobs:
       with:
         python-version: 3.9
 
-    - name: Cache pip
-      uses: actions/cache@v2
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-py3.9-${{ hashFiles('requirements.txt') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-py3.9-
-          ${{ runner.os }}-pip-
-
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel
@@ -46,9 +37,9 @@ jobs:
       run: |
         # stop the build if there are Python syntax errors or undefined names
         # For some reason we have to specifically ignore G001 as well
-        flake8 --select=E9,F63,F7,F82 --ignore=G001,G004 --show-source
+        flake8 --select=E9,F63,F7,F82 --show-source --ignore=G001,G004
         # exit-zero treats all errors as warnings.
-        flake8 --exit-zero
+        # flake8 --exit-zero
 
   # Run unit tests on Linux, OSX and Windows
   pytest:

README.rst

@@ -20,9 +20,10 @@ Installation instructions
 
   >>> git clone https://github.com/SNflows/flows.git .
 
-* All dependencies can be installed using the following command. It is recommended to do this in a dedicated `virtualenv <https://virtualenv.pypa.io/en/stable/>`_ or similar:
+* Required dependencies can be installed using the following command. It is recommended to do this in a dedicated `virtualenv <https://virtualenv.pypa.io/en/stable/>`_ or similar:
 
   >>> pip install -r requirements.txt
+  >>> pip install -r requirements_dev.txt  # for tests/development
 
 * Last step is to create a config-file. Create a file named "config.ini" and place it in the "flows" directory. Make sure that the file can only be read by you (``chmod 0600 config.ini``)!
   This file can contain all the settings for running the pipeline. A minimal file for working with the pipeline is

flows/reference_cleaning.py

@@ -88,11 +88,22 @@ def add_target(self, target: Target, starid: int = 0) -> None:
             self.xy = np.vstack(((target.pixel_column, target.pixel_row), self.xy))
 
 
-def use_sep(image: FlowsImage):
+def use_sep(image: FlowsImage, tries: int = 5, thresh: float = 5.):
+
     # Use sep to for soure extraction
     sep_background = sep.Background(image.image, mask=image.mask)
-    objects = sep.extract(image.image - sep_background, thresh=5., err=sep_background.globalrms, mask=image.mask,
-                          deblend_cont=0.1, minarea=9, clean_param=2.0)
+    try:
+        objects = sep.extract(image.image - sep_background, thresh=thresh, err=sep_background.globalrms,
+                              mask=image.mask, deblend_cont=0.1, minarea=9, clean_param=2.0)
+    except KeyboardInterrupt:
+        raise
+    except Exception:
+        logger.warning("SEP failed, trying again...")
+        if tries > 0:
+            thresh += 3
+            return use_sep(image, tries - 1, thresh * 2)
+        else:
+            raise
     return References(table=objects)
 
 

setup.cfg

@@ -9,22 +9,38 @@ extend-ignore = E203
 enable-extensions = G
 
 ignore =
-    G004, # logger does not optimizes f strings but __str__ calls are ok for us.
-	E117, # over-indented (set when using tabs)
-	E127, # continuation line over-indented for visual indent
-	E128, # continuation line under-indented for visual indent
-	E201, # whitespace after '('
-	E202, # whitespace before ')'
-	E265, # block comment should start with '# '
-	E231, # missing whitespace after ','
-	E226, # missing whitespace around arithmetic operator
-	E261, # at least two spaces before inline comment
-	E302, # expected 2 blank lines, found 1
-	E305, # expected 2 blank lines after class or function definition, found 1
-	E501, # line too long
-	E701, # multiple statements on one line (colon)
-	W503, # Line break occurred before a binary operator
-	ET128, # (flake8-tabs) unexpected number of tabs and spaces at start of XXX
+    G004,
+    # logger does not optimizes f strings but __str__ calls are ok for us.
+	E117,
+    # over-indented (set when using tabs)
+	E127,
+    # continuation line over-indented for visual indent
+	E128,
+    # continuation line under-indented for visual indent
+	E201,
+    # whitespace after '('
+	E202,
+    # whitespace before ')'
+	E265,
+    # block comment should start with '# '
+	E231,
+    # missing whitespace after ','
+	E226,
+    # missing whitespace around arithmetic operator
+	E261,
+    # at least two spaces before inline comment
+	E302,
+    # expected 2 blank lines, found 1
+	E305,
+    # expected 2 blank lines after class or function definition, found 1
+	E501,
+    # line too long
+	E701,
+    # multiple statements on one line (colon)
+	W503,
+    # Line break occurred before a binary operator
+	ET128,
+    # (flake8-tabs) unexpected number of tabs and spaces at start of XXX
 
 [tool:pytest]
 addopts = --strict-markers --durations=10