Move PypeIt's scriptbase into our utils

Having difficulties installing on the observer machines (too old) because of PypeIt's requirement of PyQt6. Since the only general use of `pypeit` is for the scripts (the scrubber still needs the full package), this commit copies the relevant pieces of PypeIt into the utils module. modified: doc/conf.py modified: doc/scripts/build_dependency_rst.py modified: obstools/__init__.py modified: obstools/deveny_collfocus.py modified: obstools/deveny_grangle.py modified: obstools/dfocus.py modified: obstools/fix_ldt_header.py modified: obstools/lmi_etc.py modified: obstools/neocp_ephem.py modified: obstools/scrub_deveny_pickup.py modified: obstools/utils.py modified: setup.cfg
LowellObservatory · Nov 10, 2023 · 1c38b78 · 1c38b78
1 parent d747050
commit 1c38b78
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Showing 12 changed files with 271 additions and 28 deletions.
diff --git a/doc/conf.py b/doc/conf.py
@@ -133,5 +133,5 @@
     "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/", None),
     "pypeit": ("https://pypeit.readthedocs.io/en/release/", None),
-    "stomp": ("https://jasonrbriggs.github.io/stomp.py/", None)
+    "stomp": ("https://jasonrbriggs.github.io/stomp.py/", None),
 }
diff --git a/doc/scripts/build_dependency_rst.py b/doc/scripts/build_dependency_rst.py
@@ -35,14 +35,19 @@ def write_dependency_table(setup_file: pathlib.Path, path: pathlib.Path):
 
     user_requires = np.sort(setup["options"]["install_requires"].split("\n")[1:])
     dev_requires = np.sort(setup["options.extras_require"]["dev"].split("\n")[1:])
+    pypeit_requires = np.sort(setup["options.extras_require"]["pypeit"].split("\n")[1:])
     required_python = setup["options"]["python_requires"]
 
-    data_table = np.empty((3, 2), dtype=object)
+    data_table = np.empty((4, 2), dtype=object)
     data_table[0, :] = ["Python Version", f"``{required_python}``"]
     data_table[1, :] = [
         "Required for users",
         ", ".join([f"``{u}``" for u in user_requires]),
     ]
+    data_table[2, :] = [
+        "Optional ``pypeit`` requirements",
+        ", ".join([f"``{u}" for u in pypeit_requires]),
+    ]
     data_table[2, :] = [
         "Required for developers",
         ", ".join([f"``{d}``" for d in dev_requires]),

diff --git a/obstools/__init__.py b/obstools/__init__.py
@@ -20,14 +20,16 @@
 from obstools.version import version
 
 # Imports for building help docs
-from obstools import deveny_collfocus
-from obstools import deveny_grangle
-from obstools import dfocus
-from obstools import lmi_etc
-from obstools import fix_ldt_header
-from obstools import neocp_ephem
-from obstools import scrub_deveny_pickup
-
+try:
+    from obstools import deveny_collfocus
+    from obstools import deveny_grangle
+    from obstools import dfocus
+    from obstools import lmi_etc
+    from obstools import fix_ldt_header
+    from obstools import neocp_ephem
+    from obstools import scrub_deveny_pickup
+except ImportError:
+    pass
 
 def short_warning(message, category, filename, lineno, file=None, line=None):
     """
@@ -53,15 +55,14 @@ def script_classes() -> dict:
         Dictionary of {name:class} for all script classes
     """
     import numpy as np
-    from pypeit.scripts import scriptbase
-    from pypeit.utils import all_subclasses
+    from obstools import utils
 
     # Recursively collect all subclasses
     # Since we use PypeIt's ScriptBase, remove all classes from that package
     scr_class = np.array(
         [
             cls
-            for cls in list(all_subclasses(scriptbase.ScriptBase))
+            for cls in list(utils.all_subclasses(utils.ScriptBase))
             if "pypeit" not in cls.name()
         ]
     )

diff --git a/obstools/deveny_collfocus.py b/obstools/deveny_collfocus.py
@@ -34,7 +34,6 @@
 
 # 3rd-Party Libraries
 import numpy as np
-from pypeit.scripts import scriptbase
 import PySimpleGUI as sg
 
 # Local Libraries
@@ -305,7 +304,7 @@ def extract_broker_values(status_dict: dict) -> tuple[str, str]:
 
 
 # Command Line Script Infrastructure (borrowed from PypeIt) ==================#
-class DevenyCollfocus(scriptbase.ScriptBase):
+class DevenyCollfocus(utils.ScriptBase):
     """Script class for ``deveny_collfocus`` tool
 
     Script structure borrowed from :class:`pypeit.scripts.scriptbase.ScriptBase`.

diff --git a/obstools/deveny_grangle.py b/obstools/deveny_grangle.py
@@ -29,7 +29,6 @@
 # 3rd-Party Libraries
 import numpy as np
 import scipy.optimize
-from pypeit.scripts import scriptbase
 import PySimpleGUI as sg
 
 # Local Libraries
@@ -374,7 +373,7 @@ def deveny_amag(grangle: float) -> float:
 
 
 # Command Line Script Infrastructure (borrowed from PypeIt) ==================#
-class DevenyGrangle(scriptbase.ScriptBase):
+class DevenyGrangle(utils.ScriptBase):
     """Script class for ``deveny_grangle`` tool
 
     Script structure borrowed from :class:`pypeit.scripts.scriptbase.ScriptBase`.

diff --git a/obstools/dfocus.py b/obstools/dfocus.py
@@ -36,7 +36,6 @@
 from matplotlib.backends.backend_pdf import PdfPages
 import matplotlib.pyplot as plt
 import numpy as np
-from pypeit.scripts import scriptbase
 import scipy.signal
 from tqdm import tqdm
 
@@ -851,7 +850,7 @@ def find_lines_in_spectrum(filename, thresh=100.0):
 
 
 # Command Line Script Infrastructure (borrowed from PypeIt) ==================#
-class DFocus(scriptbase.ScriptBase):
+class DFocus(utils.ScriptBase):
     """Script class for ``dfocus`` tool
 
     Script structure borrowed from :class:`pypeit.scripts.scriptbase.ScriptBase`.

diff --git a/obstools/fix_ldt_header.py b/obstools/fix_ldt_header.py
@@ -25,9 +25,9 @@
 
 # 3rd-Party Libraries
 import ccdproc
-from pypeit.scripts import scriptbase
 
 # Local Libraries
+from obstools import utils
 
 # CONSTANTS
 
@@ -65,7 +65,7 @@ def fix_ldt_header(files: str | pathlib.Path | list, keyword: str, new_value):
 
 
 # Command Line Script Infrastructure (borrowed from PypeIt) ==================#
-class FixLdtHeader(scriptbase.ScriptBase):
+class FixLdtHeader(utils.ScriptBase):
     """Script class for ``fix_ldt_header`` tool
 
     Script structure borrowed from :class:`pypeit.scripts.scriptbase.ScriptBase`.

diff --git a/obstools/lmi_etc.py b/obstools/lmi_etc.py
@@ -48,7 +48,6 @@
 # 3rd-Party Libraries
 import astropy.table
 import numpy as np
-from pypeit.scripts import scriptbase
 
 # Local Libraries
 from obstools import utils
@@ -530,7 +529,7 @@ def sky_count_per_sec_per_ap(
 
 
 # Command Line Script Infrastructure (borrowed from PypeIt) ==================#
-class LmiEtc(scriptbase.ScriptBase):
+class LmiEtc(utils.ScriptBase):
     """Script class for ``lmi_etc`` tool
 
     Script structure borrowed from :class:`pypeit.scripts.scriptbase.ScriptBase`.

diff --git a/obstools/neocp_ephem.py b/obstools/neocp_ephem.py
@@ -98,10 +98,10 @@
 # 3rd-Party Libraries
 import astropy.coordinates
 import astropy.units as u
-from pypeit.scripts import scriptbase
 import requests
 
 # Local Libraries
+from obstools import utils
 
 
 def neocp_ephem(neocp_id):
@@ -184,7 +184,7 @@ def neocp_ephem(neocp_id):
 
 
 # Command Line Script Infrastructure (borrowed from PypeIt) ==================#
-class NeocpEphem(scriptbase.ScriptBase):
+class NeocpEphem(utils.ScriptBase):
     """Script class for ``neocp_ephem`` tool
 
     Script structure borrowed from :class:`pypeit.scripts.scriptbase.ScriptBase`.

diff --git a/obstools/scrub_deveny_pickup.py b/obstools/scrub_deveny_pickup.py
@@ -61,7 +61,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
 from pypeit import msgs
-from pypeit.scripts import scriptbase
 import pypeit.spec2dobj
 import scipy.fft
 import scipy.ndimage
@@ -1609,7 +1608,7 @@ def pixper_tofrom_hz(val: np.ndarray) -> np.ndarray:
 
 
 # Command Line Script Infrastructure (borrowed from PypeIt) ==================#
-class ScrubDevenyPickup(scriptbase.ScriptBase):
+class ScrubDevenyPickup(utils.ScriptBase):
     """Script class for ``scrub_deveny_pickup`` tool
 
     Script structure borrowed from :class:`pypeit.scripts.scriptbase.ScriptBase`.