From 66ef3a8524b2a0374f7b52191507927970c732dd Mon Sep 17 00:00:00 2001 From: rettigl Date: Tue, 19 Dec 2023 23:08:54 +0100 Subject: [PATCH 1/4] Setup ruff as linter + formatter move mypy options into pyproject.toml Add mypy to pre-commit hooks --- .github/workflows/linting.yml | 10 +++++----- .pre-commit-config.yaml | 17 ++++++++++------- pyproject.toml | 28 ++++++++++++++++++++++++++-- sed/diagnostics.py | 4 ---- tests/test_binning.py | 8 ++++---- 5 files changed, 45 insertions(+), 22 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 0b8d2ae9..1d6c96f7 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -25,14 +25,14 @@ jobs: poetry-version: 1.2.2 # Linting steps, excute all linters even if one fails - - name: pycodestyle + - name: ruff run: - poetry run pycodestyle --ignore=E203,E501,W503 sed tests - - name: pylint + poetry run ruff sed tests + - name: ruff formating if: ${{ always() }} run: - poetry run pylint -j 0 --good-names=i,j,k,ex,x,y,t,k,v,ax,df,ec,mc,dc,ct --disable=fixme,too-many-branches,too-many-locals,too-many-statements,too-many-arguments,too-many-lines,too-many-public-methods,too-many-instance-attributes,too-few-public-methods sed tests + poetry run ruff format --check sed tests - name: mypy if: ${{ always() }} run: - poetry run mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional sed tests + poetry run mypy sed tests diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fbb2c8cc..6eb876ee 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,15 +11,18 @@ repos: - id: check-ast - id: check-docstring-first -- repo: https://github.com/psf/black - rev: 22.3.0 +- repo: https://github.com/astral-sh/ruff-pre-commit + # Ruff version. + rev: v0.1.7 hooks: - - id: black - args: [--line-length=100] -- repo: https://github.com/PyCQA/flake8 - rev: 5.0.4 + # Run the linter. + - id: ruff + # Run the formatter. + - id: ruff-format +- repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.7.1 hooks: - - id: flake8 + - id: mypy - repo: https://github.com/asottile/reorder_python_imports rev: v3.8.2 hooks: diff --git a/pyproject.toml b/pyproject.toml index efe06d90..f9e80dd7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,9 +52,8 @@ pytest = "^7.0.1" pytest-cov = "^3.0.0" pytest-xdist = "^2.5.0" pytest-clarity = "^1.0.1" -pylint = "^3.0.1" +ruff = "^0.1.7" mypy = "^1.6.0" -pycodestyle = "^2.11.1" types-pyyaml = "^6.0.12.12" types-requests = "^2.31.0.9" pyfakefs = "^5.3.0" @@ -79,3 +78,28 @@ omit = [ "config.py", "config-3.py", ] + +[tool.ruff] +include = ["pynxtools/*.py", "tests/*.py"] +select = [ + "E", # pycodestyle + "W", # pycodestyle + "PL", # pylint +] +ignore = [ + "E701", # Multiple statements on one line (colon) + "PLR0911", # Too many return statements + "PLR0912", # Too many branches + "PLR0913", # Too many arguments in function definition + "PLR0915", # Too many statements + "PLR2004", # Magic value used instead of constant +] +fixable = ["ALL"] +line-length = 100 # change the default line length number or characters. + +[tool.mypy] +strict = false +ignore_missing_imports = true +follow_imports = "silent" +no_strict_optional = true +disable_error_code = "import, annotation-unchecked" diff --git a/sed/diagnostics.py b/sed/diagnostics.py index 22e7dd6d..69985733 100644 --- a/sed/diagnostics.py +++ b/sed/diagnostics.py @@ -86,7 +86,6 @@ def grid_histogram( figsz = kwds.pop("figsize", (14, 8)) if backend == "matplotlib": - nrv = len(rvs) nrow = int(np.ceil(nrv / ncol)) histtype = kwds.pop("histtype", "step") @@ -94,7 +93,6 @@ def grid_histogram( fig, ax = plt.subplots(nrow, ncol, figsize=figsz) otherax = ax.copy() for i, zipped in enumerate(zip(rvs, rvbins, rvranges)): - # Make each histogram plot rvname, rvbin, rvrg = zipped try: @@ -131,12 +129,10 @@ def grid_histogram( fig.delaxes(oax) elif backend == "bokeh": - output_notebook(hide_banner=True) plots = [] for i, zipped in enumerate(zip(rvs, rvbins, rvranges)): - rvname, rvbin, rvrg = zipped histvals, edges = np.histogram(dct[rvname], bins=rvbin, range=rvrg) diff --git a/tests/test_binning.py b/tests/test_binning.py index 89f79f7e..78815276 100644 --- a/tests/test_binning.py +++ b/tests/test_binning.py @@ -106,7 +106,7 @@ def test_histdd_bins_as_numpy(args: Tuple[np.ndarray, np.ndarray, int]): hist1, edges1 = np.histogramdd(sample_, bins_) hist2, edges2 = numba_histogramdd(sample_, bins_) np.testing.assert_allclose(hist1, hist2) - for (edges1_, edges2_) in zip(edges1, edges2): + for edges1_, edges2_ in zip(edges1, edges2): np.testing.assert_allclose(edges1_, edges2_) @@ -139,7 +139,7 @@ def test_histdd_ranges_as_numpy(args: Tuple[np.ndarray, tuple, tuple, int]): hist1, edges1 = np.histogramdd(sample_, bins_, ranges_) hist2, edges2 = numba_histogramdd(sample_, bins_, ranges_) np.testing.assert_allclose(hist1, hist2) - for (edges1_, edges2_) in zip(edges1, edges2): + for edges1_, edges2_ in zip(edges1, edges2): np.testing.assert_allclose(edges1_, edges2_) @@ -172,7 +172,7 @@ def test_histdd_one_bins_as_numpy(args: Tuple[np.ndarray, int, tuple, int]): hist1, edges1 = np.histogramdd(sample_, bins_, ranges_) hist2, edges2 = numba_histogramdd(sample_, bins_, ranges_) np.testing.assert_allclose(hist1, hist2) - for (edges1_, edges2_) in zip(edges1, edges2): + for edges1_, edges2_ in zip(edges1, edges2): np.testing.assert_allclose(edges1_, edges2_) @@ -207,7 +207,7 @@ def test_from_bins_equals_from_bin_range( hist1, edges1 = numba_histogramdd(sample_, bins_, ranges_) hist2, edges2 = numba_histogramdd(sample_, arrays_) np.testing.assert_allclose(hist1, hist2, verbose=True) - for (edges1_, edges2_) in zip(edges1, edges2): + for edges1_, edges2_ in zip(edges1, edges2): np.testing.assert_allclose(edges1_, edges2_) From 2f5afc2404a3e3e6a11a2082c3a3ffddd5fcaebc Mon Sep 17 00:00:00 2001 From: rettigl Date: Tue, 19 Dec 2023 23:13:21 +0100 Subject: [PATCH 2/4] add ruff badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 7e38e943..b62b9809 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ Backend to handle photoelectron resolved datastreams. [![Documentation Status](https://github.com/OpenCOMPES/sed/actions/workflows/documentation.yml/badge.svg)](https://opencompes.github.io/sed/) +[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) ![](https://github.com/OpenCOMPES/sed/actions/workflows/linting.yml/badge.svg?branch=main) ![](https://github.com/OpenCOMPES/sed/actions/workflows/testing_multiversion.yml/badge.svg?branch=main) ![](https://img.shields.io/pypi/pyversions/sed-processor) From e5712adc772ff98eb3ebb224169fd187e1cc4ddd Mon Sep 17 00:00:00 2001 From: rettigl Date: Tue, 19 Dec 2023 23:16:34 +0100 Subject: [PATCH 3/4] update poetry.lock file --- poetry.lock | 723 +++++++++++++++++++++++----------------------------- 1 file changed, 316 insertions(+), 407 deletions(-) diff --git a/poetry.lock b/poetry.lock index d41ba16c..6eb8763d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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"2.0" python-versions = ">=3.8,<3.11" -content-hash = "25d3f2f67d533846273f587c96e2e6c5a3e537f43d58087135bfddb48a5e58aa" +content-hash = "8d00780234547e6ea06973f7742872f9bd3585f7497f648c86dd7b7b3f73e596" From 70c29f3f9015426f59eb3c2ce30d8460771c91a0 Mon Sep 17 00:00:00 2001 From: rettigl Date: Tue, 19 Dec 2023 23:35:40 +0100 Subject: [PATCH 4/4] add additional ruff options and correct path reformat files under sed --- pyproject.toml | 4 +++- sed/binning/binning.py | 3 --- sed/calibrator/energy.py | 8 -------- sed/calibrator/momentum.py | 5 ----- sed/core/dfops.py | 2 +- sed/core/processor.py | 4 +--- sed/io/hdf5.py | 1 - sed/loader/flash/loader.py | 1 - sed/loader/mirrorutil.py | 4 ++-- sed/loader/mpes/loader.py | 12 ++++++------ sed/loader/sxp/loader.py | 1 - 11 files changed, 13 insertions(+), 32 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f9e80dd7..cbb48fb3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -80,7 +80,7 @@ omit = [ ] [tool.ruff] -include = ["pynxtools/*.py", "tests/*.py"] +include = ["sed/*.py", "tests/*.py"] select = [ "E", # pycodestyle "W", # pycodestyle @@ -93,6 +93,8 @@ ignore = [ "PLR0913", # Too many arguments in function definition "PLR0915", # Too many statements "PLR2004", # Magic value used instead of constant + "PLR5501", # else-if-used + "PLW2901", # redefined-loop-name ] fixable = ["ALL"] line-length = 100 # change the default line length number or characters. diff --git a/sed/binning/binning.py b/sed/binning/binning.py index c57efa72..fe30320a 100644 --- a/sed/binning/binning.py +++ b/sed/binning/binning.py @@ -316,13 +316,10 @@ def bin_dataframe( # limit multithreading in worker threads with threadpool_limits(limits=threads_per_worker, user_api=threadpool_api): - # Main loop for binning for i in tqdm(range(0, df.npartitions, n_cores), disable=not pbar): - core_tasks = [] # Core-level jobs for j in range(0, n_cores): - partition_index = i + j if partition_index >= df.npartitions: break diff --git a/sed/calibrator/energy.py b/sed/calibrator/energy.py index 114618f0..c8853053 100644 --- a/sed/calibrator/energy.py +++ b/sed/calibrator/energy.py @@ -461,7 +461,6 @@ def add_ranges( newranges: List[Tuple] = [] for i in range(self.ntraces): - pathcorr = find_correspondence( traces[ref_id, :], traces[i, :], @@ -651,7 +650,6 @@ def view( # pylint: disable=dangerous-default-value sign = 1 if energy_scale == "kinetic" else -1 if backend == "matplotlib": - figsize = kwds.pop("figsize", (12, 4)) fig, ax = plt.subplots(figsize=figsize) for itr, trace in enumerate(traces): @@ -704,7 +702,6 @@ def view( # pylint: disable=dangerous-default-value ax.set_title(ttl) elif backend == "bokeh": - output_notebook(hide_banner=True) colors = it.cycle(ColorCycle[10]) ttp = [("(x, y)", "($x, $y)")] @@ -1767,7 +1764,6 @@ def normspec( specnorm = [] for i in range(nspec): - spec = specs[i] if smooth: @@ -1879,7 +1875,6 @@ def peaksearch( plt.figure(figsize=(10, 4)) for rng, trace in zip(ranges, traces.tolist()): - cond = (tof >= rng[0]) & (tof <= rng[1]) trace = np.array(trace).ravel() tofseg, trseg = tof[cond], trace[cond] @@ -1991,7 +1986,6 @@ def peakdetect1d( for index, (x, y) in enumerate( zip(x_axis[:-lookahead], y_axis[:-lookahead]), ): - if y > _max: _max = y _max_pos = x @@ -2005,7 +1999,6 @@ def peakdetect1d( # Maxima peak candidate found # look ahead in signal to ensure that this is a peak and not jitter if y_axis[index : index + lookahead].max() < _max: - max_peaks.append([_max_pos, _max]) dump.append(True) # Set algorithm to only find minima now @@ -2025,7 +2018,6 @@ def peakdetect1d( # Minima peak candidate found # look ahead in signal to ensure that this is a peak and not jitter if y_axis[index : index + lookahead].min() > _min: - min_peaks.append([_min_pos, _min]) dump.append(False) # Set algorithm to only find maxima now diff --git a/sed/calibrator/momentum.py b/sed/calibrator/momentum.py index 995d9613..17349ef1 100644 --- a/sed/calibrator/momentum.py +++ b/sed/calibrator/momentum.py @@ -250,7 +250,6 @@ def update(plane: int, width: int): ) def apply_fun(apply: bool): # pylint: disable=unused-argument - start = plane_slider.value stop = plane_slider.value + width_slider.value @@ -439,7 +438,6 @@ def feature_extract( raise ValueError("No image loaded for feature extraction!") if feature_type == "points": - # Detect the point landmarks self.peaks = po.peakdetect2d(image, **kwds) @@ -551,7 +549,6 @@ def onclick(event): cid = fig.canvas.mpl_connect("button_press_event", onclick) def apply_func(apply: bool): # pylint: disable=unused-argument - fig.canvas.mpl_disconnect(cid) point_no_input.close() @@ -1256,7 +1253,6 @@ def view( # pylint: disable=dangerous-default-value ) elif backend == "bokeh": - output_notebook(hide_banner=True) colors = it.cycle(ColorCycle[10]) ttp = [("(x, y)", "($x, $y)")] @@ -1281,7 +1277,6 @@ def view( # pylint: disable=dangerous-default-value if annotated is True: for p_keys, p_vals in points.items(): - try: xcirc, ycirc = p_vals[:, 0], p_vals[:, 1] fig.scatter( diff --git a/sed/core/dfops.py b/sed/core/dfops.py index ec29c789..7127f7f0 100644 --- a/sed/core/dfops.py +++ b/sed/core/dfops.py @@ -64,7 +64,7 @@ def apply_jitter( # jitter sizes that don't match the original bin sizes jitter = np.random.standard_normal(size=colsize) - for (col, col_jittered, amp) in zip(cols, cols_jittered, amps): + for col, col_jittered, amp in zip(cols, cols_jittered, amps): df[col_jittered] = df[col] + amp * jitter return df diff --git a/sed/core/processor.py b/sed/core/processor.py index dc5c289f..088b6b12 100644 --- a/sed/core/processor.py +++ b/sed/core/processor.py @@ -827,7 +827,6 @@ def apply_momentum_calibration( preview (bool): Option to preview the first elements of the data frame. """ if self._dataframe is not None: - print("Adding kx/ky columns to dataframe:") self._dataframe, metadata = self.mc.append_k_axis( df=self._dataframe, @@ -1049,7 +1048,6 @@ def load_bias_series( self.ec.load_data(biases=biases, traces=traces, tof=tof) elif data_files is not None: - self.ec.bin_data( data_files=cast(List[str], self.cpy(data_files)), axes=axes, @@ -1250,7 +1248,7 @@ def save_energy_calibration( filename = "sed_config.yaml" calibration = {} try: - for (key, value) in self.ec.calibration.items(): + for key, value in self.ec.calibration.items(): if key in ["axis", "refid", "Tmat", "bvec"]: continue if key == "energy_scale": diff --git a/sed/io/hdf5.py b/sed/io/hdf5.py index 47f862de..34ab0016 100644 --- a/sed/io/hdf5.py +++ b/sed/io/hdf5.py @@ -94,7 +94,6 @@ def to_h5(data: xr.DataArray, faddr: str, mode: str = "w"): saving. """ with h5py.File(faddr, mode) as h5_file: - print(f"saving data to {faddr}") # Saving data, make a single dataset diff --git a/sed/loader/flash/loader.py b/sed/loader/flash/loader.py index 8627b762..6c0b8d1b 100644 --- a/sed/loader/flash/loader.py +++ b/sed/loader/flash/loader.py @@ -45,7 +45,6 @@ class FlashLoader(BaseLoader): supported_file_types = ["h5"] def __init__(self, config: dict) -> None: - super().__init__(config=config) self.multi_index = ["trainId", "pulseId", "electronId"] self.index_per_electron: MultiIndex = None diff --git a/sed/loader/mirrorutil.py b/sed/loader/mirrorutil.py index 2be3184b..1946a171 100644 --- a/sed/loader/mirrorutil.py +++ b/sed/loader/mirrorutil.py @@ -225,7 +225,7 @@ def cleanup_oldest_scan( total_size = 0 for scan in scan_dirs: size = 0 - for (path, dirs, filenames) in os.walk( # pylint: disable=W0612 + for path, dirs, filenames in os.walk( # pylint: disable=W0612 scan, ): for sfile in filenames: @@ -240,7 +240,7 @@ def cleanup_oldest_scan( oldest_scan = None for scan in scan_dirs: size = 0 - for (path, dirs, filenames) in os.walk( # pylint: disable=W0612 + for path, dirs, filenames in os.walk( # pylint: disable=W0612 scan, ): for sfile in filenames: diff --git a/sed/loader/mpes/loader.py b/sed/loader/mpes/loader.py index da10d8ef..faeb2d10 100644 --- a/sed/loader/mpes/loader.py +++ b/sed/loader/mpes/loader.py @@ -7,12 +7,14 @@ import glob import json import os -import urllib from typing import Dict from typing import List from typing import Sequence from typing import Tuple from typing import Union +from urllib.error import HTTPError +from urllib.error import URLError +from urllib.request import urlopen import dask import dask.array as da @@ -255,7 +257,6 @@ def hdf5_to_array( # Read out groups: data_list = [] for group in group_names: - g_dataset = np.asarray(h5file[group]) if bool(data_type): g_dataset = g_dataset.astype(data_type) @@ -341,7 +342,6 @@ def hdf5_to_timed_array( data_list = [] ms_marker = np.asarray(h5file[ms_markers_group]) for group in group_names: - g_dataset = np.asarray(h5file[group]) if bool(data_type): g_dataset = g_dataset.astype(data_type) @@ -461,7 +461,7 @@ def get_archiver_data( iso_from = datetime.datetime.utcfromtimestamp(ts_from).isoformat() iso_to = datetime.datetime.utcfromtimestamp(ts_to).isoformat() req_str = archiver_url + archiver_channel + "&from=" + iso_from + "Z&to=" + iso_to + "Z" - with urllib.request.urlopen(req_str) as req: + with urlopen(req_str) as req: data = json.load(req) secs = [x["secs"] + x["nanos"] * 1e-9 for x in data[0]["data"]] vals = [x["val"] for x in data[0]["data"]] @@ -767,14 +767,14 @@ def gather_metadata( print( f"Data for channel {channel} doesn't exist for time {start}", ) - except urllib.error.HTTPError as exc: + except HTTPError as exc: print( f"Incorrect URL for the archive channel {channel}. " "Make sure that the channel name and file start and end times are " "correct.", ) print("Error code: ", exc) - except urllib.error.URLError as exc: + except URLError as exc: print( f"Cannot access the archive URL for channel {channel}. " f"Make sure that you are within the FHI network." diff --git a/sed/loader/sxp/loader.py b/sed/loader/sxp/loader.py index bdcd9b96..df5c8fe1 100644 --- a/sed/loader/sxp/loader.py +++ b/sed/loader/sxp/loader.py @@ -46,7 +46,6 @@ class SXPLoader(BaseLoader): supported_file_types = ["h5"] def __init__(self, config: dict) -> None: - super().__init__(config=config) self.multi_index = ["trainId", "pulseId", "electronId"] self.index_per_electron: MultiIndex = None