Merge pull request #275 from AstarVienna/dev_master

Release 0.6.2

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "ScopeSim"
-version = "0.6.1"
+version = "0.6.2"
 description = "Generalised telescope observation simulator"
 readme = "README.md"
 requires-python = ">=3.8"
@@ -43,13 +43,15 @@ dependencies = [
 dev = [
     "jupyter",
     "jupytext",
+    "ipykernel",
 ]
 test = [
     "pytest>=5.0.0",
     "pytest-cov",
     "scopesim_templates>=0.4.4",
     # Just so that readthedocs doesn't include the tests module - yes it's hacky
     "skycalc_cli",
+    "ipykernel",
 ]
 docs = [
     "sphinx>=4.3.0",
@@ -59,6 +61,7 @@ docs = [
     "nbsphinx",
     "numpydoc",
     "scopesim_templates>=0.4.4",
+    "ipykernel"
 ]
 
 [project.urls]

scopesim/commands/user_commands.py

@@ -155,11 +155,10 @@ def __init__(self, **kwargs):
 
     def update(self, **kwargs):
         """
-        Updates the current parameters with a yaml dictionary
+        Update the current parameters with a yaml dictionary.
 
         See the ``UserCommands`` main docstring for acceptable kwargs
         """
-
         if "use_instrument" in kwargs:
             self.package_name = kwargs["use_instrument"]
             self.update(packages=[kwargs["use_instrument"]],
@@ -279,10 +278,9 @@ def _repr_pretty_(self, p, cycle):
         else:
             p.text(str(self))
 
+
 def check_for_updates(package_name):
-    """
-    Asks IRDB server if there are newer versions of the instrument package
-    """
+    """Ask IRDB server if there are newer versions of instrument package."""
     response = {}
 
     # tracking **exclusively** your IP address for our internal stats
@@ -298,7 +296,7 @@ def check_for_updates(package_name):
 
 
 def patch_fake_symlinks(path: Path):
-    """Fixes broken symlinks in path.
+    """Fix broken symlinks in path.
 
     The irdb has some symlinks in it, which work fine under linux, but not
     always under windows, see https://stackoverflow.com/a/11664406 .
@@ -345,7 +343,7 @@ def patch_fake_symlinks(path: Path):
 
 def add_packages_to_rc_search(local_path, package_list):
     """
-    Adds the paths of a list of locally saved packages to the search path list
+    Add the paths of a list of locally saved packages to the search path list.
 
     Parameters
     ----------
@@ -375,7 +373,7 @@ def add_packages_to_rc_search(local_path, package_list):
 
 def load_yaml_dicts(filename):
     """
-    Loads one or more dicts stored in a YAML file under ``filename``
+    Load one or more dicts stored in a YAML file under `filename`.
 
     Parameters
     ----------
@@ -388,7 +386,6 @@ def load_yaml_dicts(filename):
         A list of dicts
 
     """
-
     yaml_dicts = []
     with open(filename) as f:
         yaml_dicts += [dic for dic in yaml.full_load_all(f)]
@@ -398,7 +395,7 @@ def load_yaml_dicts(filename):
 
 def list_local_packages(action="display"):
     """
-    Lists the packages on the local disk that ScopeSim can find
+    List the packages on the local disk that ScopeSim can find.
 
     Packages can only be found in the directory listed under::
 
@@ -428,7 +425,6 @@ def list_local_packages(action="display"):
         If action="return": Lists containing the names of locally saved packages
 
     """
-
     local_path = Path(rc.__config__["!SIM.file.local_packages_path"]).absolute()
     pkgs = [d for d in local_path.iterdir() if d.is_dir()]
 

scopesim/detector/detector_array.py

@@ -21,7 +21,7 @@ def __init__(self, detector_list=None, **kwargs):
 
     def readout(self, image_planes, array_effects=None, dtcr_effects=None, **kwargs):
         """
-        Read out the detector array into a FITS file
+        Read out the detector array into a FITS file.
 
         Parameters
         ----------
@@ -39,7 +39,6 @@ def readout(self, image_planes, array_effects=None, dtcr_effects=None, **kwargs)
         self.latest_exposure : fits.HDUList
 
         """
-
         # .. note:: Detector is what used to be called Chip
         #           DetectorArray is the old Detector
 
@@ -95,8 +94,6 @@ def readout(self, image_planes, array_effects=None, dtcr_effects=None, **kwargs)
         for effect in self.array_effects:
             image_plane = effect.apply_to(image_plane, **self.meta)
 
-
-
         self.latest_exposure = hdu_list
 
         return self.latest_exposure
@@ -110,15 +107,15 @@ def __str__(self):
         return f"{self.__class__.__name__} with {self.detector_list!s}"
 
     def _repr_pretty_(self, p, cycle):
-        """For ipython"""
+        """For ipython."""
         if cycle:
             p.text(f"{self.__class__.__name__}(...)")
         else:
             p.text(str(self))
 
 
 def make_primary_hdu(meta):
-    """Create the primary header from meta data"""
+    """Create the primary header from meta data."""
     new_meta = utils.stringify_dict(meta)
     prihdu = fits.PrimaryHDU()
     prihdu.header.update(new_meta)

scopesim/effects/apertures.py

@@ -1,4 +1,4 @@
-"""Effects related to field masks, including spectroscopic slits"""
+"""Effects related to field masks, including spectroscopic slits."""
 
 from pathlib import Path
 import logging
@@ -20,7 +20,7 @@
 
 class ApertureMask(Effect):
     """
-    Only provides the on-sky window coords of the Aperture
+    Only provides the on-sky window coords of the Aperture.
 
     - Case: Imaging
         - Covers the whole FOV of the detector
@@ -75,6 +75,7 @@ class ApertureMask(Effect):
         An integer to identify the ``ApertureMask`` in a list of apertures
 
     """
+
     def __init__(self, **kwargs):
         if not np.any([key in kwargs for key in ["filename", "table",
                                                  "array_dict"]]):
@@ -107,9 +108,12 @@ def __init__(self, **kwargs):
         check_keys(kwargs, self.required_keys, "warning", all_any="any")
 
     def apply_to(self, obj, **kwargs):
+        """See parent docstring."""
         if isinstance(obj, FOVSetupBase):
-            x = quantity_from_table("x", self.table, u.arcsec).to(u.arcsec).value
-            y = quantity_from_table("y", self.table, u.arcsec).to(u.arcsec).value
+            x = quantity_from_table("x", self.table,
+                                    u.arcsec).to(u.arcsec).value
+            y = quantity_from_table("y", self.table,
+                                    u.arcsec).to(u.arcsec).value
             obj.shrink(["x", "y"], ([min(x), max(x)], [min(y), max(y)]))
 
             # ..todo: HUGE HACK - Get rid of this!
@@ -121,7 +125,7 @@ def apply_to(self, obj, **kwargs):
 
     # Outdated. Remove when removing all old FOVManager code from effects
     def fov_grid(self, which="edges", **kwargs):
-        """ Returns a header with the sky coordinates """
+        """Return a header with the sky coordinates."""
         logging.warning("DetectorList.fov_grid will be depreciated in v1.0")
         if which == "edges":
             self.meta.update(kwargs)
@@ -162,7 +166,7 @@ def mask(self):
 
     def get_mask(self):
         """
-        For placing over FOVs if the Aperture is rotated w.r.t. the field
+        For placing over FOVs if the Aperture is rotated w.r.t. the field.
         """
         self.meta = from_currsys(self.meta)
 
@@ -193,8 +197,8 @@ def plot(self, axes=None):
 class RectangularApertureMask(ApertureMask):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
-        params = {"x_unit" : "arcsec",
-                  "y_unit" : "arcsec"}
+        params = {"x_unit": "arcsec",
+                  "y_unit": "arcsec"}
         self.meta.update(params)
         self.meta.update(kwargs)
         check_keys(self.meta, ["x", "y", "width", "height"])
@@ -226,7 +230,7 @@ def get_table(self, **kwargs):
 
 class ApertureList(Effect):
     """
-    A list of apertures, useful for IFU or MOS instruments
+    A list of apertures, useful for IFU or MOS instruments.
 
     Parameters
     ----------
@@ -255,9 +259,9 @@ class ApertureList(Effect):
     optional column ``offset`` may be added. This column describes the offset
     from 0 deg to the angle where the first corner is set.
 
-    Additionally, the filename of an ``ApertureMask`` polygon file can be given.
-    The geometry of the polygon defined in the file will be scaled to fit
-    inside the edges of the row.
+    Additionally, the filename of an ``ApertureMask`` polygon file can be
+    given. The geometry of the polygon defined in the file will be scaled to
+    fit inside the edges of the row.
 
     .. note:: ``shape`` values ``"rect"`` and ``4`` do not produce equal results
 
@@ -269,6 +273,7 @@ class ApertureList(Effect):
 
 
     """
+
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
         params = {"pixel_scale": "!INST.pixel_scale",
@@ -287,11 +292,12 @@ def __init__(self, **kwargs):
             check_keys(self.table.colnames, required_keys)
 
     def apply_to(self, obj, **kwargs):
+        """See parent docstring."""
         if isinstance(obj, FOVSetupBase):
             new_vols = []
             for row in self.table:
                 vols = obj.extract(["x", "y"], ([row["left"], row["right"]],
-                                                [row["bottom"], row["top"] ]))
+                                                [row["bottom"], row["top"]]))
                 for vol in vols:
                     vol["meta"]["aperture_id"] = row["id"]
 
@@ -380,10 +386,9 @@ def __add__(self, other):
     #     return self.get_apertures(item)[0]
 
 
-
 class SlitWheel(Effect):
     """
-    A selection of predefined spectroscopic slits and possibly other field masks
+    Selection of predefined spectroscopic slits and possibly other field masks.
 
     It should contain an open position.
     A user can define a non-standard slit by directly using the Aperture
@@ -448,14 +453,15 @@ def __init__(self, **kwargs):
         self.table = self.get_table()
 
     def apply_to(self, obj, **kwargs):
-        """Use apply_to of current_slit"""
+        """Use apply_to of current_slit."""
         return self.current_slit.apply_to(obj, **kwargs)
 
     def fov_grid(self, which="edges", **kwargs):
+        """See parent docstring."""
         return self.current_slit.fov_grid(which=which, **kwargs)
 
     def change_slit(self, slitname=None):
-        """Change the current slit"""
+        """Change the current slit."""
         if not slitname or slitname in self.slits.keys():
             self.meta["current_slit"] = slitname
             self.include = slitname
@@ -464,13 +470,13 @@ def change_slit(self, slitname=None):
 
     def add_slit(self, newslit, name=None):
         """
-        Add a slit to the SlitWheel
+        Add a slit to the SlitWheel.
 
         Parameters
-        ==========
+        ----------
         newslit : Slit
         name : string
-           Name to be used for the new slit. If `None`, a name from
+           Name to be used for the new slit. If ``None``, a name from
            the newslit object is used.
         """
         if name is None:
@@ -479,7 +485,7 @@ def add_slit(self, newslit, name=None):
 
     @property
     def current_slit(self):
-        """Return the currently used slit"""
+        """Return the currently used slit."""
         currslit = from_currsys(self.meta["current_slit"])
         if not currslit:
             return False
@@ -490,7 +496,7 @@ def __getattr__(self, item):
 
     def get_table(self):
         """
-        Create a table of slits with centre position, width and length
+        Create a table of slits with centre position, width and length.
 
         Width is defined as the extension in the y-direction, length in the
         x-direction. All values are in milliarcsec.
@@ -519,7 +525,7 @@ def get_table(self):
         return tbl
 
 
-################################################################################
+###############################################################################
 
 
 def make_aperture_polygon(left, right, top, bottom, angle, shape, **kwargs):
@@ -577,7 +583,8 @@ def mask_from_coords(x, y, pixel_scale):
 
 
 def rotate(x, y, x0, y0, angle):
-    """ Rotate a line by ``angle`` [deg] around the point (x0, y0) """
+    """Rotate a line by `angle` [deg] around the point (`x0`, `y0`)."""
+    # TODO: isn't that just a rotation matrix?
     angle_rad = angle / 57.29578
     xnew = x0 + (x - x0) * np.cos(angle_rad) - (y - y0) * np.sin(angle_rad)
     ynew = y0 + (x - x0) * np.sin(angle_rad) + (y - y0) * np.cos(angle_rad)