Tweaks (#84)

Author: fsoubelet

docs/release.rst

@@ -222,10 +222,10 @@ def plot_envelope(
         twiss_hr["dispersive_envelope_x"] = twiss_hr.dx * beam_params.deltap_p
         twiss_hr["dispersive_envelope_y"] = twiss_hr.dy * beam_params.deltap_p
         twiss_hr["envelope_x"] = np.sqrt(
-            twiss_hr.betatronic_envelope_x ** 2 + (twiss_hr.dx * beam_params.deltap_p) ** 2
+            twiss_hr.betatronic_envelope_x**2 + (twiss_hr.dx * beam_params.deltap_p) ** 2
         )
         twiss_hr["envelope_y"] = np.sqrt(
-            twiss_hr.betatronic_envelope_y ** 2 + (twiss_hr.dy * beam_params.deltap_p) ** 2
+            twiss_hr.betatronic_envelope_y**2 + (twiss_hr.dy * beam_params.deltap_p) ** 2
         )
         machine = twiss_hr[twiss_hr.apertype == "ellipse"]
 
@@ -1226,7 +1226,6 @@ def plot_machine_layout(
                     height=dipole.k1l,
                     v_offset=dipole.k1l / 2,
                     color="r",
-                    alpha=0.3,
                     **kwargs,
                 )
             plotted_elements += 1

pyhdtoolkit/cpymadtools/plotters.py

@@ -11,11 +11,11 @@
 BASE_LATTICE = LatticeGenerator.generate_base_cas_lattice()
 CURRENT_DIR = pathlib.Path(__file__).parent
 INPUTS_DIR = CURRENT_DIR / "inputs"
-LHC_SEQUENCE = INPUTS_DIR / "lhc_as-built.seq"
-LHC_OPTICS = INPUTS_DIR / "opticsfile.22"
-LHC_INJ_OPTICS = INPUTS_DIR / "opticsfile.1"
-LHC_B1_APERTURE = INPUTS_DIR / "aperture.b1.madx"
-LHC_B1_APERTOL = INPUTS_DIR / "aper_tol.b1.madx"
+LHC_SEQUENCE = INPUTS_DIR / "madx" / "lhc_as-built.seq"
+LHC_OPTICS = INPUTS_DIR / "madx" / "opticsfile.22"
+LHC_INJ_OPTICS = INPUTS_DIR / "madx" / "opticsfile.1"
+LHC_B1_APERTURE = INPUTS_DIR / "madx" / "aperture.b1.madx"
+LHC_B1_APERTOL = INPUTS_DIR / "madx" / "aper_tol.b1.madx"
 
 # ----- Fixtures for cpymadtools tests ----- #
 

tests/conftest.py

@@ -345,14 +345,14 @@ def test_get_bpms_coupling_rdts(self, _non_matched_lhc_madx, _reference_twiss_rd
 
 @pytest.fixture()
 def _magnets_fields_path() -> pathlib.Path:
-    return INPUTS_DIR / "magnets_fields.tfs"
+    return INPUTS_DIR / "cpymadtools" / "magnets_fields.tfs"
 
 
 @pytest.fixture()
 def _correct_bpms_list() -> pathlib.Path:
-    return INPUTS_DIR / "correct_bpms_list.pkl"
+    return INPUTS_DIR / "cpymadtools" / "correct_bpms_list.pkl"
 
 
 @pytest.fixture()
 def _reference_twiss_rdts() -> pathlib.Path:
-    return INPUTS_DIR / "twiss_with_rdts.tfs"
+    return INPUTS_DIR / "cpymadtools" / "twiss_with_rdts.tfs"

tests/inputs/ampdet.tfs tests/inputs/cpymadtools/ampdet.tfs

@@ -28,7 +28,7 @@
 
 CURRENT_DIR = pathlib.Path(__file__).parent
 INPUTS_DIR = CURRENT_DIR.parent / "inputs"
-GUIDO_LATTICE = INPUTS_DIR / "guido_lattice.madx"
+GUIDO_LATTICE = INPUTS_DIR / "cpymadtools" / "guido_lattice.madx"
 BASE_LATTICE = LatticeGenerator.generate_base_cas_lattice()
 
 

tests/inputs/correct_bpms_list.pkl tests/inputs/cpymadtools/correct_bpms_list.pkl

@@ -93,14 +93,14 @@ def test_single_particle_ptc_track_with_onepass(self, _matched_base_lattice):
 
 @pytest.fixture()
 def _ampdet_tfs_path() -> pathlib.Path:
-    return INPUTS_DIR / "ampdet.tfs"
+    return INPUTS_DIR / "cpymadtools" / "ampdet.tfs"
 
 
 @pytest.fixture()
 def _rdts_tfs_path() -> pathlib.Path:
-    return INPUTS_DIR / "rdts.tfs"
+    return INPUTS_DIR / "cpymadtools" / "rdts.tfs"
 
 
 @pytest.fixture()
 def _ptc_twiss_tfs_path() -> pathlib.Path:
-    return INPUTS_DIR / "ptc_twiss.tfs"
+    return INPUTS_DIR / "cpymadtools" / "ptc_twiss.tfs"

tests/inputs/dynap.tfs tests/inputs/cpymadtools/dynap.tfs

@@ -105,9 +105,9 @@ def test_get_footprint_patches_raises_wrong_shape(self, _dynap_tfs_path, caplog)
 
 @pytest.fixture()
 def _plottable_footprint_path() -> pathlib.Path:
-    return INPUTS_DIR / "plottable_footprint.npz"
+    return INPUTS_DIR / "cpymadtools" / "plottable_footprint.npz"
 
 
 @pytest.fixture()
 def _dynap_tfs_path() -> pathlib.Path:
-    return INPUTS_DIR / "dynap.tfs"
+    return INPUTS_DIR / "cpymadtools" / "dynap.tfs"

tests/inputs/guido_lattice.madx tests/inputs/cpymadtools/guido_lattice.madx

@@ -32,7 +32,7 @@ def test_get_ips_twiss(self, _ips_twiss_path, _matched_lhc_madx):
     def test_get_irs_twiss(self, ir, _matched_lhc_madx):
         madx = _matched_lhc_madx
 
-        reference_df = tfs.read(INPUTS_DIR / f"ir{ir:d}_twiss.tfs")
+        reference_df = tfs.read(INPUTS_DIR / "cpymadtools" / f"ir{ir:d}_twiss.tfs")
         ir_df = get_ir_twiss(madx, ir=ir)
         # assert_dict_equal(reference_df.headers, ir_df.headers)  # bugged at the moment
         assert_frame_equal(reference_df.set_index("name"), ir_df.set_index("name"))
@@ -47,9 +47,9 @@ def test_get_irs_twiss(self, ir, _matched_lhc_madx):
 
 @pytest.fixture()
 def _ips_twiss_path() -> pathlib.Path:
-    return INPUTS_DIR / "ips_twiss.tfs"
+    return INPUTS_DIR / "cpymadtools" / "ips_twiss.tfs"
 
 
 @pytest.fixture()
 def _twiss_export() -> pathlib.Path:
-    return INPUTS_DIR / "twiss_export.tfs"
+    return INPUTS_DIR / "cpymadtools" / "twiss_export.tfs"

tests/inputs/ips_twiss.tfs tests/inputs/cpymadtools/ips_twiss.tfs

@@ -211,14 +211,14 @@ def _create_2d_gaussian_noise(mean: float, stdev: float, shape: tuple) -> np.nda
 
 @pytest.fixture()
 def _to_scale() -> np.ndarray:
-    return np.load(INPUTS_DIR / "to_scale.npy")
+    return np.load(INPUTS_DIR / "maths" / "to_scale.npy")
 
 
 @pytest.fixture()
 def _scaled() -> np.ndarray:
-    return np.load(INPUTS_DIR / "scaled.npy")
+    return np.load(INPUTS_DIR / "maths" / "scaled.npy")
 
 
 @pytest.fixture()
 def _force_scaled() -> np.ndarray:
-    return np.load(INPUTS_DIR / "force_scaled.npy")
+    return np.load(INPUTS_DIR / "maths" / "force_scaled.npy")

tests/inputs/ir1_twiss.tfs tests/inputs/cpymadtools/ir1_twiss.tfs

@@ -10,12 +10,12 @@
 CURRENT_DIR = pathlib.Path(__file__).parent
 INPUTS_DIR = CURRENT_DIR / "inputs"
 INPUT_PATHS = {
-    "alpha_beta": INPUTS_DIR / "alpha_beta.npy",
-    "u_vector": INPUTS_DIR / "u_vector.npy",
-    "u_bar": INPUTS_DIR / "u_bar.npy",
-    "beta11": INPUTS_DIR / "beta11.npy",
-    "beta21": INPUTS_DIR / "beta21.npy",
-    "lebedev": INPUTS_DIR / "lebedev_size.npy",
+    "alpha_beta": INPUTS_DIR / "optics" / "alpha_beta.npy",
+    "u_vector": INPUTS_DIR / "optics" / "u_vector.npy",
+    "u_bar": INPUTS_DIR / "optics" / "u_bar.npy",
+    "beta11": INPUTS_DIR / "optics" / "beta11.npy",
+    "beta21": INPUTS_DIR / "optics" / "beta21.npy",
+    "lebedev": INPUTS_DIR / "optics" / "lebedev_size.npy",
 }
 
 

tests/inputs/ir5_twiss.tfs tests/inputs/cpymadtools/ir5_twiss.tfs

@@ -38,7 +38,7 @@
 
 
 def _square(integer: int) -> int:
-    return integer ** 2
+    return integer**2
 
 
 def _to_str(integer: int) -> str:
@@ -416,7 +416,7 @@ class TestMultiProcessorExecutor:
         "function, inputs, results",
         [
             (_square, list(range(6)), [0, 1, 4, 9, 16, 25]),
-            (_square, [10 * i for i in range(10)], [e ** 2 for e in [10 * i for i in range(10)]]),
+            (_square, [10 * i for i in range(10)], [e**2 for e in [10 * i for i in range(10)]]),
             (_to_str, list(range(6)), [str(e) for e in range(6)]),
             (_to_str, [10 * i for i in range(10)], [str(e) for e in [10 * i for i in range(10)]]),
         ],
@@ -435,7 +435,7 @@ class TestMultiThreaderExecutor:
         "function, inputs, results",
         [
             (_square, list(range(6)), [0, 1, 4, 9, 16, 25]),
-            (_square, [10 * i for i in range(10)], [e ** 2 for e in [10 * i for i in range(10)]]),
+            (_square, [10 * i for i in range(10)], [e**2 for e in [10 * i for i in range(10)]]),
             (_to_str, list(range(6)), [str(e) for e in range(6)]),
             (_to_str, [10 * i for i in range(10)], [str(e) for e in [10 * i for i in range(10)]]),
         ],
@@ -674,13 +674,13 @@ def _taskless_condor_q_output() -> str:
 
 @pytest.fixture()
 def _correct_user_tasks() -> List[HTCTaskSummary]:
-    pickle_file_path = INPUTS_DIR / "correct_user_tasks.pkl"
+    pickle_file_path = INPUTS_DIR / "utils" / "correct_user_tasks.pkl"
     with pickle_file_path.open("rb") as file:
         return pickle.load(file)
 
 
 @pytest.fixture()
 def _correct_cluster_summary() -> ClusterSummary:
-    pickle_file_path = INPUTS_DIR / "correct_cluster_summary.pkl"
+    pickle_file_path = INPUTS_DIR / "utils" / "correct_cluster_summary.pkl"
     with pickle_file_path.open("rb") as file:
         return pickle.load(file)