[pre-commit] pre-commit autoupdate (#498)

Co-authored-by: Patrick Schuenke <[email protected]>
PTB-MR · Nov 5, 2024 · bc830f5 · bc830f5 · github-actions · Nov 5, 2024
1 parent eeb9233
commit bc830f5
Show file tree

Hide file tree

Showing 9 changed files with 49 additions and 46 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-docstring-first
@@ -15,14 +15,14 @@ repos:
       - id: mixed-line-ending
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.7.2
     hooks:
       - id: ruff # linter
         args: [--fix]
       - id: ruff-format # formatter
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.25.0
+    rev: v1.27.0
     hooks:
       - id: typos
 
@@ -34,7 +34,7 @@ repos:
         exclude: ^tests/
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.13.0
     hooks:
       - id: mypy
         pass_filenames: false

diff --git a/examples/direct_reconstruction.ipynb b/examples/direct_reconstruction.ipynb
@@ -37,10 +37,10 @@
     "\n",
     "import requests\n",
     "\n",
-    "data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')\n",
-    "response = requests.get(zenodo_url + fname, timeout=30)\n",
-    "data_file.write(response.content)\n",
-    "data_file.flush()"
+    "with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:\n",
+    "    response = requests.get(zenodo_url + fname, timeout=30)\n",
+    "    data_file.write(response.content)\n",
+    "    data_file.flush()"
    ]
   },
   {

diff --git a/examples/direct_reconstruction.py b/examples/direct_reconstruction.py
@@ -11,10 +11,10 @@
 
 import requests
 
-data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')
-response = requests.get(zenodo_url + fname, timeout=30)
-data_file.write(response.content)
-data_file.flush()
+with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:
+    response = requests.get(zenodo_url + fname, timeout=30)
+    data_file.write(response.content)
+    data_file.flush()
 
 # %% [markdown]
 # ### Image reconstruction

diff --git a/examples/iterative_sense_reconstruction.ipynb b/examples/iterative_sense_reconstruction.ipynb
@@ -37,10 +37,10 @@
     "\n",
     "import requests\n",
     "\n",
-    "data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')\n",
-    "response = requests.get(zenodo_url + fname, timeout=30)\n",
-    "data_file.write(response.content)\n",
-    "data_file.flush()"
+    "with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:\n",
+    "    response = requests.get(zenodo_url + fname, timeout=30)\n",
+    "    data_file.write(response.content)\n",
+    "    data_file.flush()"
    ]
   },
   {

diff --git a/examples/iterative_sense_reconstruction.py b/examples/iterative_sense_reconstruction.py
@@ -11,10 +11,10 @@
 
 import requests
 
-data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')
-response = requests.get(zenodo_url + fname, timeout=30)
-data_file.write(response.content)
-data_file.flush()
+with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:
+    response = requests.get(zenodo_url + fname, timeout=30)
+    data_file.write(response.content)
+    data_file.flush()
 
 # %% [markdown]
 # ### Image reconstruction

diff --git a/examples/pulseq_2d_radial_golden_angle.ipynb b/examples/pulseq_2d_radial_golden_angle.ipynb
@@ -33,13 +33,14 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "d16f41f1",
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "outputs": [],
    "source": [
     "# define zenodo records URL and create a temporary directory and h5-file\n",
     "zenodo_url = 'https://zenodo.org/records/10854057/files/'\n",
-    "fname = 'pulseq_radial_2D_402spokes_golden_angle_with_traj.h5'\n",
-    "data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')"
+    "fname = 'pulseq_radial_2D_402spokes_golden_angle_with_traj.h5'"
    ]
   },
   {
@@ -50,9 +51,10 @@
    "outputs": [],
    "source": [
     "# Download raw data using requests\n",
-    "response = requests.get(zenodo_url + fname, timeout=30)\n",
-    "data_file.write(response.content)\n",
-    "data_file.flush()"
+    "with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:\n",
+    "    response = requests.get(zenodo_url + fname, timeout=30)\n",
+    "    data_file.write(response.content)\n",
+    "    data_file.flush()"
    ]
   },
   {
@@ -125,10 +127,10 @@
     "# download the sequence file from zenodo\n",
     "zenodo_url = 'https://zenodo.org/records/10868061/files/'\n",
     "seq_fname = 'pulseq_radial_2D_402spokes_golden_angle.seq'\n",
-    "seq_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.seq')\n",
-    "response = requests.get(zenodo_url + seq_fname, timeout=30)\n",
-    "seq_file.write(response.content)\n",
-    "seq_file.flush()"
+    "with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.seq') as seq_file:\n",
+    "    response = requests.get(zenodo_url + seq_fname, timeout=30)\n",
+    "    seq_file.write(response.content)\n",
+    "    seq_file.flush()"
    ]
   },
   {

diff --git a/examples/pulseq_2d_radial_golden_angle.py b/examples/pulseq_2d_radial_golden_angle.py
@@ -19,13 +19,14 @@
 # define zenodo records URL and create a temporary directory and h5-file
 zenodo_url = 'https://zenodo.org/records/10854057/files/'
 fname = 'pulseq_radial_2D_402spokes_golden_angle_with_traj.h5'
-data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')
+
 
 # %%
 # Download raw data using requests
-response = requests.get(zenodo_url + fname, timeout=30)
-data_file.write(response.content)
-data_file.flush()
+with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:
+    response = requests.get(zenodo_url + fname, timeout=30)
+    data_file.write(response.content)
+    data_file.flush()
 
 # %% [markdown]
 # ### Image reconstruction using KTrajectoryIsmrmrd
@@ -62,10 +63,10 @@
 # download the sequence file from zenodo
 zenodo_url = 'https://zenodo.org/records/10868061/files/'
 seq_fname = 'pulseq_radial_2D_402spokes_golden_angle.seq'
-seq_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.seq')
-response = requests.get(zenodo_url + seq_fname, timeout=30)
-seq_file.write(response.content)
-seq_file.flush()
+with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.seq') as seq_file:
+    response = requests.get(zenodo_url + seq_fname, timeout=30)
+    seq_file.write(response.content)
+    seq_file.flush()
 
 # %%
 # Read raw data and calculate trajectory using KTrajectoryPulseq

diff --git a/examples/regularized_iterative_sense_reconstruction.ipynb b/examples/regularized_iterative_sense_reconstruction.ipynb
@@ -37,10 +37,10 @@
     "\n",
     "import requests\n",
     "\n",
-    "data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')\n",
-    "response = requests.get(zenodo_url + fname, timeout=30)\n",
-    "data_file.write(response.content)\n",
-    "data_file.flush()"
+    "with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:\n",
+    "    response = requests.get(zenodo_url + fname, timeout=30)\n",
+    "    data_file.write(response.content)\n",
+    "    data_file.flush()"
    ]
   },
   {

diff --git a/examples/regularized_iterative_sense_reconstruction.py b/examples/regularized_iterative_sense_reconstruction.py
@@ -11,10 +11,10 @@
 
 import requests
 
-data_file = tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5')
-response = requests.get(zenodo_url + fname, timeout=30)
-data_file.write(response.content)
-data_file.flush()
+with tempfile.NamedTemporaryFile(mode='wb', delete=False, suffix='.h5') as data_file:
+    response = requests.get(zenodo_url + fname, timeout=30)
+    data_file.write(response.content)
+    data_file.flush()
 
 # %% [markdown]
 # ### Image reconstruction
File	Stmts	Miss	Cover	Missing
src/mrpro/algorithms/csm
inati.py	24	1	96%	44
walsh.py	16	1	94%	34
src/mrpro/algorithms/dcf
dcf_voronoi.py	53	4	92%	15, 48–49, 76
src/mrpro/algorithms/optimizers
adam.py	20	1	95%	69
src/mrpro/algorithms/reconstruction
DirectReconstruction.py	28	16	43%	51–71, 85
IterativeSENSEReconstruction.py	13	1	92%	76
Reconstruction.py	50	22	56%	42, 54–56, 80–87, 104–113
RegularizedIterativeSENSEReconstruction.py	41	17	59%	96–100, 114–139
src/mrpro/data
AcqInfo.py	128	2	98%	174, 214
CsmData.py	29	3	90%	15, 82–84
DcfData.py	45	8	82%	18, 66, 78–83
IData.py	67	9	87%	119, 125, 129, 159–167
IHeader.py	75	7	91%	75, 109, 127–131
KHeader.py	165	17	90%	25, 127–131, 158, 210, 221, 228–229, 232, 239, 278–289
KNoise.py	31	15	52%	39–52, 56–61
KTrajectory.py	69	5	93%	178–182
MoveDataMixin.py	127	18	86%	15, 110, 126, 140–142, 203, 265–267, 280, 359, 379–380, 382, 397–398, 400
QData.py	39	7	82%	42, 65–73
Rotation.py	674	36	95%	100, 198, 335, 433, 477, 495, 581, 583, 592, 626, 628, 691, 768, 773, 776, 791, 808, 813, 889, 1077, 1082, 1085, 1109, 1113, 1240, 1242, 1250–1251, 1315, 1397, 1608, 1690, 1846, 1881, 1885, 1996
SpatialDimension.py	246	23	91%	34, 104, 119, 126, 132, 167, 177, 294–296, 309–311, 345, 363, 376, 389, 402, 415, 424–425, 440, 449
TrajectoryDescription.py	14	1	93%	23
acq_filters.py	10	1	90%	47
src/mrpro/data/_kdata
KData.py	105	16	85%	108–109, 118, 126, 180–181, 216, 221–222, 241–252
KDataRemoveOsMixin.py	29	2	93%	44, 46
KDataSelectMixin.py	21	2	90%	48, 64
KDataSplitMixin.py	49	3	94%	51, 81, 90
src/mrpro/data/traj_calculators
KTrajectoryCalculator.py	25	2	92%	23, 45
KTrajectoryIsmrmrd.py	13	2	85%	41, 50
KTrajectoryPulseq.py	29	1	97%	54
src/mrpro/operators
CartesianSamplingOp.py	50	9	82%	49–50, 55–56, 61–62, 88, 91, 114
ConstraintsOp.py	60	2	97%	46, 48
EndomorphOperator.py	65	2	97%	228, 234
FiniteDifferenceOp.py	27	2	93%	40, 105
FourierOp.py	77	1	99%	131
Functional.py	71	5	93%	20–22, 117, 119
GridSamplingOp.py	136	9	93%	72–73, 82–83, 90–91, 94, 96, 98
LinearOperator.py	171	12	93%	55, 91, 190, 220, 261, 270, 278, 287, 295, 320, 418, 423
LinearOperatorMatrix.py	158	16	90%	82, 119, 152, 161, 166, 175–178, 191–194, 203, 215, 304, 331, 359
MultiIdentityOp.py	13	2	85%	43, 48
Operator.py	78	2	97%	25, 74
ProximableFunctionalSeparableSum.py	39	3	92%	50, 103, 110
SliceProjectionOp.py	173	8	95%	44, 61, 63, 69, 206, 227, 260, 300
WaveletOp.py	120	5	96%	152, 170, 205, 210, 233
ZeroPadOp.py	16	1	94%	30
src/mrpro/utils
filters.py	62	2	97%	44, 49
modify_acq_info.py	17	1	94%	12
slice_profiles.py	46	6	87%	20, 36, 113–116, 149
sliding_window.py	34	1	97%	34
split_idx.py	10	2	80%	43, 47
summarize_tensorvalues.py	11	9	18%	20–29
typing.py	18	11	39%	8–23
zero_pad_or_crop.py	31	6	81%	26, 30, 54, 57, 60, 63
TOTAL	4709	360	92%