Update ruff and bumpversion configs

CITATION.cff

@@ -27,5 +27,5 @@ doi: "10.5281/zenodo.1090388"
 license: "BSD-3-Clause"
 message: "If you use this software, please cite it using these metadata."
 title: Instamatic
-version: "2.0.1"
+version: "2.0.2"
 ...

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 # https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
 [project]
 name = "instamatic"
-version = "2.0.1"
+version = "2.0.2"
 description = "Python program for automated electron diffraction data collection"
 readme = "README.md"
 requires-python = ">=3.7"
@@ -125,19 +125,14 @@ target-version = 'py37'
 line-length = 96
 
 [tool.ruff.lint]
-# Enable Pyflakes `E` and `F` codes by default.
 select = [
- 'F', # Pyflakes
- 'E', # pycodestyle (error)
- 'W', # pycodestyle (warning)
- 'I', # isort
- 'UP', # pyupgrade
- 'A', # flake8-builtins
- 'COM', # flake8-commas
- 'C4', # flake8-comprehensions
- 'TID', # flake8-tidy-imports
- 'NPY201', # numpy deprecation
+ "F", # Pyflakes
+ "E", # pycodestyle (error)
+ "W", # pycodestyle (warning)
+ "I", # isort
+ "NPY201", # numpy deprecations
 ]
+
 ignore = [
  'F401',
  'F403',
@@ -148,38 +143,27 @@ ignore = [
  'A003',
 ]
 
+[tool.ruff.lint.isort]
+known-first-party = ['instamatic']
 
-# Allow autofix for all enabled rules (when `--fix`) is provided.
-fixable = ['A', 'B', 'C', 'D', 'E', 'F', 'I', 'UP', 'BLE', 'COM', 'C4', 'TID',]
-unfixable = []
+[tool.ruff.format]
+quote-style = "single"
+indent-style = "space"
 
-exclude = [
- '.bzr',
- '.direnv',
- '.eggs',
- '.git',
- '.hg',
- '.mypy_cache',
- '.nox',
- '.pants.d',
- '.ruff_cache',
- '.svn',
- '.tox',
- '.venv',
- '__pypackages__',
- '_build',
- 'buck-out',
- 'build',
- 'dist',
- 'node_modules',
- 'venv',
- '.venv',
- 'scripts',
-]
-per-file-ignores = {}
+[tool.bumpversion]
+current_version = "2.0.2"
 
-# Allow unused variables when underscore-prefixed.
-dummy-variable-rgx = '^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$'
+[[tool.bumpversion.files]]
+filename = "src/instamatic/__init__.py"
+search = "__version__ = '{current_version}'"
+replace = "__version__ = '{new_version}'"
 
-[tool.ruff.lint.isort]
-known-first-party = ['instamatic']
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = "version = \"{current_version}\""
+replace = "version = \"{new_version}\""
+
+[[tool.bumpversion.files]]
+filename = "CITATION.cff"
+search = "version: {current_version}"
+replace = "version: {new_version}"

src/instamatic/__init__.py

@@ -9,7 +9,7 @@
 # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 """
 
-__version__ = '2.0.1'
+__version__ = '2.0.2'
 __title__ = 'instamatic'
 __long_title__ = f'{__title__} v{__version__}'
 __author__ = 'Stef Smeets'

src/instamatic/camera/camera_timepix.py

@@ -171,7 +171,7 @@ def read_pixels_cfg(self, filename):
  sys.exit()
 
  def process_real_dac(self, chipnr=None, index=None, key=None, value=None):
- """int *chipnr."""
+ """Int *chipnr."""
  'int *index'
  'std::string *key'
  'std::string *value'
@@ -237,7 +237,7 @@ def enable_timer(self, enable, us):
  After the Relaxd shutter opens (either explicitly by software or by an
  external trigger), it closes again after the set time.
 
- bool enable
+ bool enable 
  int us = 10 # microseconds
  """
  enable = c_bool(enable)
@@ -258,7 +258,7 @@ def set_acq_pars(self, pars):
  self.lib.EMCameraObj_setAcqPars(self.obj, byref(pars))
 
  def is_busy(self, busy):
- """bool *busy."""
+ """Bool *busy."""
  busy = c_bool(busy)
  self.lib.EMCameraObj_isBusy(self.obj, byref(busy))
 

src/instamatic/experiments/autocred/experiment.py

@@ -325,7 +325,8 @@ def img_var(self, img, apert_pos):
  return np.var(img)
 
  def check_img_outsidebeam_byscale(self, img1_scale, img2_scale):
- """`img1` is the original image for reference, `img2` is the new image."""
+ """`img1` is the original image for reference, `img2` is the new
+ image."""
  if img2_scale / img1_scale < 0.5 or img2_scale / img1_scale > 2:
  return 1
  else:
@@ -595,15 +596,6 @@ def auto_cred_collection(self, path, pathtiff, pathsmv, pathred, transform_imgsh
 
  img0, h = self.defocus_and_image(difffocus=self.diff_defocus, exp_t=self.exposure_time_image)
 
- """if trackmethod == "p":
- shift = self.tracking_by_particlerecog(img0)
- delta_beamshiftcoord = np.matmul(self.calib_beamshift.transform, shift)
- self.logger.debug("Beam shift coordinates: {}".format(delta_beamshiftcoord))
-
- bs_x0, bs_y0 = self.setandupdate_bs(bs_x0, bs_y0, delta_beamshiftcoord)
-
- img0, h = self.defocus_and_image(difffocus = self.diff_defocus, exp_t = self.exposure_time_image)"""
-
  img0_p = preprocess(img0.astype(float))
  scorefromCNN = predict(img0_p)
  # self.print_and_log(logger = self.logger, msg = "Score for the DP: {}".format(scorefromCNN))
@@ -645,8 +637,8 @@ def auto_cred_collection(self, path, pathtiff, pathsmv, pathred, transform_imgsh
  numb_robustTrack = 0
  """Turn on and off for crystal movement guess here."""
  self.guess_crystmove = False
-
- """set acquisition time to be around 0.52 s in order to fix the image interval times."""
+ """Set acquisition time to be around 0.52 s in order to fix the image
+ interval times."""
  acquisition_time = self.expt + 0.02
 
  self.ctrl.cam.block()
@@ -665,8 +657,8 @@ def auto_cred_collection(self, path, pathtiff, pathsmv, pathred, transform_imgsh
  numb_robustTrack += 1
  else:
  self.image_interval = self.nom_ii
-
- """If variance changed over 20%, do a robust check to ensure crystal is back"""
+ """If variance changed over 20%, do a robust check to
+ ensure crystal is back."""
 
  if imgvar / img0var < 0.5 or imgvar / img0var > 2 or imgscale / imgscale0 > 1.15 or imgscale / imgscale0 < 0.85:
  self.image_interval = self.robust_ii
@@ -683,8 +675,8 @@ def auto_cred_collection(self, path, pathtiff, pathsmv, pathred, transform_imgsh
 
  if i % self.image_interval == 0: # aim to make this more dynamically adapted...
  t_start = time.perf_counter()
-
- """Guessing the next particle position by simply apply the same beamshift change as previous"""
+ """Guessing the next particle position by simply apply the
+ same beamshift change as previous."""
  if self.guess_crystmove and i >= self.nom_ii:
  bs_x0, bs_y0 = self.setandupdate_bs(bs_x0, bs_y0, delta_beamshiftcoord)
 
@@ -701,8 +693,8 @@ def auto_cred_collection(self, path, pathtiff, pathsmv, pathred, transform_imgsh
  imgvar = self.img_var(img_cropped, crystal_pos)
 
  self.logger.debug(f'Image variance: {imgvar}')
-
- """If variance changed over 50%, then the crystal is outside the beam and stop data collection"""
+ """If variance changed over 50%, then the crystal is
+ outside the beam and stop data collection."""
  if imgvar / img0var < 0.2 or imgvar / img0var > 5:
  self.print_and_del('Collection stopping because crystal out of the beam...')
  self.stopEvent.set()

src/instamatic/server/vm_ubuntu_server.py

@@ -36,11 +36,9 @@ def start_vm_process(vmname=VM_ID, vmachine_pwd=VM_PWD, time_delay=VM_DELAY1, mo
  machine = vbox.find_machine(vmname)
  progress = machine.launch_vm_process(session, mode, '')
  progress.wait_for_completion()
-
- """wait for certain sec to ensure a normal vm startup"""
+ """Wait for certain sec to ensure a normal vm startup."""
  time.sleep(time_delay)
-
- """assume vm is password protected"""
+ """Assume vm is password protected."""
  session.console.keyboard.put_keys(vmachine_pwd)
  session.console.keyboard.put_keys(['ENTER'])
  print('password delivered!')
@@ -117,8 +115,8 @@ def vm_ubuntu_start_xds_AtFolder(session, conn, shelxt, unitcell, spgr, composit
 
  session.console.keyboard.put_keys('xds')
  session.console.keyboard.put_keys(['ENTER'])
-
- """Not sure if I should put some delay here, but just to avoid neglected communication"""
+ """Not sure if I should put some delay here, but just to avoid
+ neglected communication."""
  time.sleep(120)
 
  if shelxt: