Nisar feature branch v11: extended csxtools to AXIS detector data

.flake8

@@ -5,5 +5,8 @@ exclude =
     build,
     dist,
     versioneer.py,
-    doc/conf.py
-max-line-length = 115
+    csxtools/doc/conf.py
+    *.ipynb_checkpoints,
+
+max-line-length = 140
+ignore = E203, W503

.github/workflows/_test-in-conda-env.yml

@@ -61,6 +61,11 @@ jobs:
     - name: Check out the code repo
       uses: actions/checkout@v4
 
+    - name: Workaround: Fix .condarc MultipleKeysError
+      run: |
+        sed -i '/auto_activate_base/d' /home/runner/.condarc || true
+        sed -i '/auto_activate:/d' /home/runner/.condarc || true
+
     - name: Set up Python ${{ inputs.python-version }} with conda
       uses: conda-incubator/setup-miniconda@v3
       with:

.github/workflows/tests.yml

@@ -9,15 +9,15 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
       fail-fast: false
     steps:
 
     - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -39,7 +39,7 @@ jobs:
         coverage xml
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml 
         flags: unittests

MANIFEST.in

@@ -1,7 +1,20 @@
+# Metadata and versioning
+include README.md
+include LICENSE.txt
+include versioneer.py
+include csxtools/_version.py
+
+# Requirements
 include requirements.txt
 include requirements-extras.txt
 
-include versioneer.py
-include csxtools/_version.py
+# Source code
+recursive-include csxtools *.py *.so
+
+# C sources and headers
+recursive-include src *.c *.h
+
+# Documentation and notebooks
+recursive-include doc *
+recursive-include examples *.ipynb
 
-recursive-include src * *.[hc]

README.md

@@ -1,11 +1,11 @@
 CSX Data Analysis Tools
 =======================
 
-
-
-[![Build Status](https://travis-ci.org/NSLS-II-CSX/csxtools.svg?branch=master)](https://travis-ci.org/NSLS-II-CSX/csxtools)
-[![Coverage Status](https://coveralls.io/repos/NSLS-II-CSX/csxtools/badge.svg?branch=master&service=github)](https://coveralls.io/github/NSLS-II-CSX/csxtools?branch=master)
-[![Code Health](https://landscape.io/github/NSLS-II-CSX/csxtools/master/landscape.svg?style=flat)](https://landscape.io/github/NSLS-II-CSX/csxtools/master)
+[![Unit Tests](https://github.com/NSLS-II-CSX/csxtools/actions/workflows/tests.yml/badge.svg)](https://github.com/NSLS-II-CSX/csxtools/actions/workflows/tests.yml)
+[![codecov](https://codecov.io/gh/NSLS-II-CSX/csxtools/branch/master/graph/badge.svg)](https://codecov.io/gh/NSLS-II-CSX/csxtools)
+[![PyPI version](https://badge.fury.io/py/csxtools.svg)](https://badge.fury.io/py/csxtools)
+[![License: BSD-3-Clause](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
+[![Downloads](https://pepy.tech/badge/csxtools)](https://pepy.tech/project/csxtools)
 
 Python library for tools to be used at the Coherent Soft X-ray scattering 
 beamline at NSLS-II, (CSX, 23-ID)

csxtools/__init__.py

@@ -1,9 +1,17 @@
 # Now import useful functions
 
-from .utils import (get_fastccd_images, get_fastccd_timestamps)  # noqa F401
+from .utils import get_fastccd_images  # noqa: F401
+from .utils import get_fastccd_flatfield  # noqa: F401
+from .utils import get_fastccd_timestamps  # noqa: F401
+
+from .utils import get_axis_images  # noqa: F401
+from .utils import get_axis_flatfield  # noqa: F401
+from .utils import get_axis_timestamps  # noqa: F401
+
 from .plotting import make_panel_plot  # noqa F401
 
 # set version string using versioneer
 from ._version import get_versions
-__version__ = get_versions()['version']
+
+__version__ = get_versions()["version"]
 del get_versions

csxtools/_version.py

@@ -1,4 +1,3 @@
-
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -57,6 +56,7 @@ def decorate(f):
             HANDLERS[vcs] = {}
         HANDLERS[vcs][method] = f
         return f
+
     return decorate
 
 
@@ -67,9 +67,12 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
         try:
             dispcmd = str([c] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen([c] + args, cwd=cwd, stdout=subprocess.PIPE,
-                                 stderr=(subprocess.PIPE if hide_stderr
-                                         else None))
+            p = subprocess.Popen(
+                [c] + args,
+                cwd=cwd,
+                stdout=subprocess.PIPE,
+                stderr=(subprocess.PIPE if hide_stderr else None),
+            )
             break
         except EnvironmentError:
             e = sys.exc_info()[1]
@@ -99,12 +102,17 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     dirname = os.path.basename(root)
     if not dirname.startswith(parentdir_prefix):
         if verbose:
-            print("guessing rootdir is '%s', but '%s' doesn't start with "
-                  "prefix '%s'" % (root, dirname, parentdir_prefix))
+            print(
+                "guessing rootdir is '%s', but '%s' doesn't start with "
+                "prefix '%s'" % (root, dirname, parentdir_prefix)
+            )
         raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
-    return {"version": dirname[len(parentdir_prefix):],
-            "full-revisionid": None,
-            "dirty": False, "error": None}
+    return {
+        "version": dirname[len(parentdir_prefix) :],
+        "full-revisionid": None,
+        "dirty": False,
+        "error": None,
+    }
 
 
 @register_vcs_handler("git", "get_keywords")
@@ -144,7 +152,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
+    tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)])
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %d
@@ -153,27 +161,32 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r'\d', r)])
+        tags = set([r for r in refs if re.search(r"\d", r)])
         if verbose:
-            print("discarding '%s', no digits" % ",".join(refs-tags))
+            print("discarding '%s', no digits" % ",".join(refs - tags))
     if verbose:
         print("likely tags: %s" % ",".join(sorted(tags)))
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix):]
+            r = ref[len(tag_prefix) :]
             if verbose:
                 print("picking %s" % r)
-            return {"version": r,
-                    "full-revisionid": keywords["full"].strip(),
-                    "dirty": False, "error": None
-                    }
+            return {
+                "version": r,
+                "full-revisionid": keywords["full"].strip(),
+                "dirty": False,
+                "error": None,
+            }
     # no suitable tags, so version is "0+unknown", but full hex is still there
     if verbose:
         print("no suitable tags, using unknown + full revision id")
-    return {"version": "0+unknown",
-            "full-revisionid": keywords["full"].strip(),
-            "dirty": False, "error": "no suitable tags"}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": keywords["full"].strip(),
+        "dirty": False,
+        "error": "no suitable tags",
+    }
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
@@ -193,9 +206,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         GITS = ["git.cmd", "git.exe"]
     # if there is a tag, this yields TAG-NUM-gHEX[-dirty]
     # if there are no tags, this yields HEX[-dirty] (no NUM)
-    describe_out = run_command(GITS, ["describe", "--tags", "--dirty",
-                                      "--always", "--long"],
-                               cwd=root)
+    describe_out = run_command(
+        GITS, ["describe", "--tags", "--dirty", "--always", "--long"], cwd=root
+    )
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
@@ -218,17 +231,16 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     dirty = git_describe.endswith("-dirty")
     pieces["dirty"] = dirty
     if dirty:
-        git_describe = git_describe[:git_describe.rindex("-dirty")]
+        git_describe = git_describe[: git_describe.rindex("-dirty")]
 
     # now we have TAG-NUM-gHEX or HEX
 
     if "-" in git_describe:
         # TAG-NUM-gHEX
-        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
+        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
         if not mo:
             # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = ("unable to parse git-describe output: '%s'"
-                               % describe_out)
+            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
             return pieces
 
         # tag
@@ -237,10 +249,12 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
-                               % (full_tag, tag_prefix))
+            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
+                full_tag,
+                tag_prefix,
+            )
             return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix):]
+        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
 
         # distance: number of commits since tag
         pieces["distance"] = int(mo.group(2))
@@ -251,8 +265,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     else:
         # HEX: no tags
         pieces["closest-tag"] = None
-        count_out = run_command(GITS, ["rev-list", "HEAD", "--count"],
-                                cwd=root)
+        count_out = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
         pieces["distance"] = int(count_out)  # total number of commits
 
     return pieces
@@ -281,8 +294,7 @@ def render_pep440(pieces):
                 rendered += ".dirty"
     else:
         # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
-                                          pieces["short"])
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
@@ -389,10 +401,12 @@ def render_git_describe_long(pieces):
 
 def render(pieces, style):
     if pieces["error"]:
-        return {"version": "unknown",
-                "full-revisionid": pieces.get("long"),
-                "dirty": None,
-                "error": pieces["error"]}
+        return {
+            "version": "unknown",
+            "full-revisionid": pieces.get("long"),
+            "dirty": None,
+            "error": pieces["error"],
+        }
 
     if not style or style == "default":
         style = "pep440"  # the default
@@ -412,8 +426,12 @@ def render(pieces, style):
     else:
         raise ValueError("unknown style '%s'" % style)
 
-    return {"version": rendered, "full-revisionid": pieces["long"],
-            "dirty": pieces["dirty"], "error": None}
+    return {
+        "version": rendered,
+        "full-revisionid": pieces["long"],
+        "dirty": pieces["dirty"],
+        "error": None,
+    }
 
 
 def get_versions():
@@ -426,8 +444,7 @@ def get_versions():
     verbose = cfg.verbose
 
     try:
-        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
-                                          verbose)
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose)
     except NotThisMethod:
         pass
 
@@ -436,12 +453,15 @@ def get_versions():
         # versionfile_source is the relative path from the top of the source
         # tree (where the .git directory might live) to this file. Invert
         # this to find the root from __file__.
-        for i in cfg.versionfile_source.split('/'):
+        for i in cfg.versionfile_source.split("/"):
             root = os.path.dirname(root)
     except NameError:
-        return {"version": "0+unknown", "full-revisionid": None,
-                "dirty": None,
-                "error": "unable to find root of source tree"}
+        return {
+            "version": "0+unknown",
+            "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to find root of source tree",
+        }
 
     try:
         pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
@@ -455,6 +475,9 @@ def get_versions():
     except NotThisMethod:
         pass
 
-    return {"version": "0+unknown", "full-revisionid": None,
-            "dirty": None,
-            "error": "unable to compute version"}
+    return {
+        "version": "0+unknown",
+        "full-revisionid": None,
+        "dirty": None,
+        "error": "unable to compute version",
+    }

csxtools/axis1/__init__.py

@@ -0,0 +1,9 @@
+from .images import correct_images_axis
+
+__all__ = ["correct_images_axis"]
+
+# set version string using versioneer
+from .._version import get_versions
+
+__version__ = get_versions()["version"]
+del get_versions