Merge pull request #114 from pllim/setup-cleanup-🧹

MNT: Infrastructure update

.bandit.yaml

@@ -0,0 +1,2 @@
+exclude_dirs:
+  - acstools/tests

.gitignore

@@ -35,6 +35,8 @@ sdist
 develop-eggs
 .installed.cfg
 distribute-*.tar.gz
+pip-wheel-metadata/
+acstools/version.py
 
 # Other
 .cache

.readthedocs.yml

@@ -12,9 +12,10 @@ python:
   version: 3.7
   system_packages: true
   install:
-    - requirements: doc/rtd-pip-requirements
-    - method: setuptools
+    - method: pip
       path: .
+      extra_requirements:
+        - docs
 
 # Don't build any extra formats
 formats: []

CHANGES.rst

@@ -0,0 +1 @@
+See https://github.com/spacetelescope/acstools/releases

Jenkinsfile

@@ -8,25 +8,18 @@ bc1.name = "release"
 // Would be nice if Jenkins can access /grp/hst/cdbs/xxxx directly.
 bc1.env_vars = ['TEST_BIGDATA=https://bytesalad.stsci.edu/artifactory']
 bc1.conda_channels = ['http://ssb.stsci.edu/astroconda']
-bc1.conda_packages = ['python=3.6',
-                      'requests',
-                      'numpy',
-                      'matplotlib',
-                      'scipy',
-                      'stsci.tools']
-bc1.build_cmds = ["pip install scikit-image ci-watson",
-                  "python setup.py install"]
+bc1.conda_packages = ['python=3.6']
+bc1.build_cmds = ["pip install -e .[test,all]"]
 bc1.test_cmds = ["pytest --basetemp=tests_output --junitxml results.xml --bigdata -v"]
 bc1.failedUnstableThresh = 1
 bc1.failedFailureThresh = 6
 
-// Run with astropy dev and Python 3.7
+// Run with astropy dev and Python 3.8
 bc2 = utils.copy(bc1)
 bc2.name = "dev"
-bc2.conda_packages[0] = "python=3.7"
-bc2.build_cmds = ["pip install scikit-image ci-watson",
-                  "pip install git+https://github.com/astropy/astropy.git#egg=astropy --upgrade --no-deps",
-                  "python setup.py install"]
+bc2.conda_packages[0] = "python=3.8"
+bc2.build_cmds = ["pip install git+https://github.com/astropy/astropy.git#egg=astropy --upgrade --no-deps",
+                  "pip install -e .[test,all]"]
 
 // Iterate over configurations that define the (distibuted) build matrix.
 // Spawn a host of the given nodetype for each combination and run in parallel.

JenkinsfileRT

@@ -14,25 +14,18 @@ bc.name = "release"
 bc.env_vars = ['TEST_BIGDATA=https://bytesalad.stsci.edu/artifactory',
                'jref=/grp/hst/cdbs/jref/']
 bc.conda_channels = ['http://ssb.stsci.edu/astroconda']
-bc.conda_packages = ['python=3.6',
-                     'requests',
-                     'numpy',
-                     'matplotlib',
-                     'scipy',
-                     'stsci.tools']
-bc.build_cmds = ["pip install scikit-image ci-watson",
-                 "python setup.py install"]
+bc.conda_packages = ['python=3.6']
+bc.build_cmds = ["pip install -e .[test,all]"]
 bc.test_cmds = ["pytest --basetemp=tests_output --junitxml results.xml --bigdata --slow -v"]
 bc.failedUnstableThresh = 1
 bc.failedFailureThresh = 6
 
-// Astropy dev and Python 3.7
+// Astropy dev and Python 3.8
 bc1 = utils.copy(bc)
 bc1.name = "dev"
-bc1.conda_packages[0] = "python=3.7"
-bc1.build_cmds = ["pip install scikit-image",
-                  "pip install git+https://github.com/astropy/astropy.git#egg=astropy --upgrade --no-deps",
-                  "python setup.py install"]
+bc1.conda_packages[0] = "python=3.8"
+bc1.build_cmds = ["pip install git+https://github.com/astropy/astropy.git#egg=astropy --upgrade --no-deps",
+                  "pip install -e .[test,all]"]
 
 // Iterate over configurations that define the (distributed) build matrix.
 // Spawn a host (or workdir) for each combination and run in parallel.

LICENSE.md

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2018, Space Telescope Science Institute, AURA
+Copyright (c) 2020, Space Telescope Science Institute, AURA
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

MANIFEST.in

@@ -1,6 +1,8 @@
 include README.rst
 include LICENSE.txt
+include CHANGES.rst
 include setup.cfg
+include pyproject.toml
 recursive-include doc *
 
 prune build

acstools/__init__.py

@@ -1,31 +1,21 @@
-"""The acstools package holds Python tasks useful for analyzing ACS data.
-
-These tasks include:
-
-Utility and library functions used by these tasks are also included in this
-module.
-
-"""
-from pkg_resources import get_distribution, DistributionNotFound
-
-
+"""The acstools package holds Python tasks useful for analyzing ACS data."""
 try:
-    __version__ = get_distribution(__name__).version
-except DistributionNotFound:
+    from .version import version as __version__
+except ImportError:
     # package is not installed
-    __version__ = 'unknown'
+    __version__ = ''
 
 
-from . import acs_destripe
-from . import acs_destripe_plus
-from . import calacs
-from . import acsccd
-from . import acscte
-from . import acscteforwardmodel
-from . import acs2d
-from . import acsrej
-from . import acssum
-from . import acszpt
-from . import acsphotcte
-from . import satdet
-from . import utils_calib
+from . import acs_destripe  # noqa
+from . import acs_destripe_plus  # noqa
+from . import calacs  # noqa
+from . import acsccd  # noqa
+from . import acscte  # noqa
+from . import acscteforwardmodel  # noqa
+from . import acs2d  # noqa
+from . import acsrej  # noqa
+from . import acssum  # noqa
+from . import acszpt  # noqa
+from . import acsphotcte  # noqa
+from . import satdet  # noqa
+from . import utils_calib  # noqa

acstools/acs2d.py

@@ -13,7 +13,7 @@
 """
 # STDLIB
 import os
-import subprocess
+import subprocess  # nosec
 
 __taskname__ = "acs2d"
 __version__ = "2.0"
@@ -98,4 +98,4 @@ def acs2d(input, exec_path='', time_stamps=False, verbose=False, quiet=False,
     if exe_args:
         call_list.extend(exe_args)
 
-    subprocess.check_call(call_list)
+    subprocess.check_call(call_list)  # nosec

acstools/acs_destripe.py

@@ -241,10 +241,10 @@ def clean(input, suffix, stat="pmode1", maxiter=15, sigrej=2.0,
         background in image rows:
 
         * 'pmode1' - SEXTRACTOR-like mode estimate based on a
-          modified `Pearson's rule <http://en.wikipedia.org/wiki/Nonparametric_skew#Pearson.27s_rule>`_:
+          modified `Pearson's rule <https://en.wikipedia.org/wiki/Nonparametric_skew#Pearson.27s_rule>`_:
           ``2.5*median-1.5*mean``;
         * 'pmode2' - mode estimate based on
-          `Pearson's rule <http://en.wikipedia.org/wiki/Nonparametric_skew#Pearson.27s_rule>`_:
+          `Pearson's rule <https://en.wikipedia.org/wiki/Nonparametric_skew#Pearson.27s_rule>`_:
           ``3*median-2*mean``;
         * 'mean' - the mean of the distribution of the "good" pixels (after
           clipping, masking, etc.);
@@ -690,7 +690,9 @@ def getcorr(): return (SMedian)
         def getcorr():
             imstat = ImageStats(image.science[i][BMask], 'mode',
                                 lower=lower, upper=upper, nclip=0)
-            assert(imstat.npix == NPix)
+            if imstat.npix != NPix:
+                raise ValueError('imstate.npix ({}) != NPix ({})'.format(
+                    imstat.npix, NPix))
             return (imstat.mode)
 
     elif stat == 'midpt':
@@ -700,7 +702,9 @@ def getcorr():
         def getcorr():
             imstat = ImageStats(image.science[i][BMask], 'midpt',
                                 lower=lower, upper=upper, nclip=0)
-            assert(imstat.npix == NPix)
+            if imstat.npix != NPix:
+                raise ValueError('imstate.npix ({}) != NPix ({})'.format(
+                    imstat.npix, NPix))
             return (imstat.midpt)
 
     nmax_rpt = 1 if rpt_clean is None else max(1, rpt_clean+1)

acstools/acs_destripe_plus.py

@@ -61,7 +61,7 @@
 # STDLIB
 import logging
 import os
-import subprocess
+import subprocess  # nosec
 
 # ASTROPY
 from astropy.time import Time
@@ -135,10 +135,10 @@ def destripe_plus(inputfile, suffix='strp', stat='pmode1', maxiter=15,
         background in image rows:
 
         * 'pmode1' - SEXTRACTOR-like mode estimate based on a
-          modified `Pearson's rule <http://en.wikipedia.org/wiki/Nonparametric_skew#Pearson.27s_rule>`_:
+          modified `Pearson's rule <https://en.wikipedia.org/wiki/Nonparametric_skew#Pearson.27s_rule>`_:
           ``2.5*median-1.5*mean``;
         * 'pmode2' - mode estimate based on
-          `Pearson's rule <http://en.wikipedia.org/wiki/Nonparametric_skew#Pearson.27s_rule>`_:
+          `Pearson's rule <https://en.wikipedia.org/wiki/Nonparametric_skew#Pearson.27s_rule>`_:
           ``3*median-2*mean``;
         * 'mean' - the mean of the distribution of the "good" pixels (after
           clipping, masking, etc.);
@@ -366,7 +366,7 @@ def destripe_plus(inputfile, suffix='strp', stat='pmode1', maxiter=15,
         raise ValueError("Both 'scimask1' and 'scimask2' must be specified "
                          "or not specified together.")
 
-    calacs_str = subprocess.check_output(['calacs.e', '--version']).split()[0]
+    calacs_str = subprocess.check_output(['calacs.e', '--version']).split()[0]  # nosec # noqa
     calacs_ver = [int(x) for x in calacs_str.decode().split('.')]
     if calacs_ver < [8, 3, 1]:
         raise ValueError('CALACS {0} is incomptible. '

acstools/acsccd.py

@@ -17,7 +17,7 @@
 """
 # STDLIB
 import os
-import subprocess
+import subprocess  # nosec
 
 __taskname__ = "acsccd"
 __version__ = "2.0"
@@ -112,4 +112,4 @@ def acsccd(input, exec_path='', time_stamps=False, verbose=False, quiet=False,
     #if biascorr:
     #    call_list.append('-bias')
 
-    subprocess.check_call(call_list)
+    subprocess.check_call(call_list)  # nosec

acstools/acscte.py

@@ -19,7 +19,7 @@
 """
 # STDLIB
 import os
-import subprocess
+import subprocess  # nosec
 
 __taskname__ = "acscte"
 __version__ = "1.0"
@@ -99,4 +99,4 @@ def acscte(input, exec_path='', time_stamps=False, verbose=False, quiet=False,
     if exe_args:
         call_list.extend(exe_args)
 
-    subprocess.check_call(call_list)
+    subprocess.check_call(call_list)  # nosec

acstools/acscteforwardmodel.py

@@ -23,7 +23,7 @@
 """
 # STDLIB
 import os
-import subprocess
+import subprocess  # nosec
 
 __taskname__ = "acscteforwardmodel"
 __version__ = "1.0"
@@ -103,4 +103,4 @@ def acscteforwardmodel(input, exec_path='', time_stamps=False, verbose=False,
     if exe_args:
         call_list.extend(exe_args)
 
-    subprocess.check_call(call_list)
+    subprocess.check_call(call_list)  # nosec

acstools/acsphotcte.py

@@ -200,21 +200,18 @@ def _check_inputs(self, **inputs):
                         return key
         # the last step is to ensure all the iterable inputs are the same length
         nl = "\n"
-        try:
-            # First we check if there were any iterable inputs
-            if iterable_lengths:
-                # if there are we make sure theyre all the same size
-                assert len(set(iterable_lengths)) == 1
-        except AssertionError:
+        # First we check if there were any iterable inputs.
+        # If there are, we make sure theyre all the same size.
+        if iterable_lengths and len(set(iterable_lengths)) != 1:
             iterable_lengths = list(map(str, iterable_lengths))
             msg = (
                 "Iterable inputs are not the same length.\n"
                 f"Computed lengths:\n{nl.join(iterable_lengths)}"
             )
             LOG.error(msg)
             return
-        else:
-            return inputs
+
+        return inputs
 
     def correct_photometry(
             self,

acstools/acsrej.py

@@ -13,7 +13,7 @@
 """
 # STDLIB
 import os
-import subprocess
+import subprocess  # nosec
 import warnings
 
 __taskname__ = "acsrej"
@@ -186,4 +186,4 @@ def acsrej(input, output, exec_path='', time_stamps=False, verbose=False,
     if exe_args:
         call_list.extend(exe_args)
 
-    subprocess.check_call(call_list)
+    subprocess.check_call(call_list)  # nosec

acstools/acssum.py

@@ -13,7 +13,7 @@
 """
 # STDLIB
 import os
-import subprocess
+import subprocess  # nosec
 
 __taskname__ = "acssum"
 __version__ = "1.0"
@@ -89,4 +89,4 @@ def acssum(input, output, exec_path='', time_stamps=False, verbose=False,
     if exe_args:
         call_list.extend(exe_args)
 
-    subprocess.check_call(call_list)
+    subprocess.check_call(call_list)  # nosec

acstools/acszpt.py

@@ -290,8 +290,10 @@ def _submit_request(self):
         attribute.
 
         """
+        if not self._url.startswith('http'):
+            raise ValueError(f'Invalid URL {self._url}')
         try:
-            self._response = urlopen(self._url)
+            self._response = urlopen(self._url)  # nosec
         except URLError as e:
             msg = ('{}\n{}\nThe query failed! Please check your inputs. '
                    'If the error persists, submit a ticket to the '

acstools/calacs.py

@@ -12,7 +12,7 @@
 
 """
 import os
-import subprocess
+import subprocess  # nosec
 
 __all__ = ['calacs']
 
@@ -93,4 +93,4 @@ def calacs(input_file, exec_path=None, time_stamps=False, temp_files=False,
     if exe_args:
         call_list.extend(exe_args)
 
-    subprocess.check_call(call_list)
+    subprocess.check_call(call_list)  # nosec