Merge 4758a61 into cec48f2

.pre-commit-config.yaml

@@ -1,14 +1,14 @@
 repos:
 -   repo: https://github.com/psf/black
-    rev: 22.1.0
+    rev: 22.12.0
     hooks:
     - id: black
       language_version: python3
       args: # arguments to configure black
         - --line-length=79
 
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.4.0
     hooks:
     # Identify invalid files
     - id: check-ast

CHANGELOG.rst

@@ -1,11 +1,21 @@
+Version 0.3.9
+-------------
+
+:Date: 12 Jan 2023
+
+* `@cylammarco <https://github.com/cylammarco>`__:
+
+  * Fixed atlas overwriting when provided sequentially
+  * Capping the numpy version to 1.23.X
+
 Version 0.3.8
 -------------
 
 :Date: 29 Nov 2022
 
 * `@cylammarco <https://github.com/cylammarco>`__:
 
-  * Fix wrong MANIFEST path
+  * Fixed wrong MANIFEST path
 
 Version 0.3.7
 -------------

README.md

@@ -23,11 +23,12 @@ More background information can be referred to this [arXiv article](https://ui.a
 
 
 ## Dependencies
-* python >= 3.6
-* numpy
-* scipy
-* pynverse
-* matplotlib
+* python >= 3.7
+* numpy>=1.16,<1.24
+* scipy>=1.3.3
+* pynverse>=0.1.4
+* matplotlib>=3.0.3
+* tqdm>=4.48.0
 
 ## Optional Dependencies
 * [plotly](https://github.com/plotly/plotly.py) >= 4.0

requirements.txt

@@ -1,5 +1,5 @@
 matplotlib>=3.0.3
-numpy>=1.16
+numpy>=1.16,<1.24
 pynverse>=0.1.4
 scipy>=1.3.3
 tqdm>=4.48.0

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = rascal
-version = 0.3.8.1
+version = 0.3.9
 license = BSD-3-Clause
 license_files = LICENSE
 description = A library for automated spectrometer wavelength calibration.
@@ -16,7 +16,6 @@ download_url = https://github.com/jveitchmichaelis/rascal
 classifiers =
     License :: OSI Approved :: BSD License
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
@@ -32,7 +31,7 @@ packages = find:
 include_package_data = True
 python_requires = >=3.6
 install_requires =
-    numpy>=1.16
+    numpy>=1.16,<1.24
     scipy>=1.3.3
     pynverse>=0.1.4
     matplotlib>=3.0.3

src/rascal/calibrator.py

@@ -1438,19 +1438,36 @@ def add_atlas(
 
             max_atlas_wavelength = self.max_wavelength + self.range_tolerance
 
-        new_atlas = Atlas(
-            elements,
-            min_atlas_wavelength=min_atlas_wavelength,
-            max_atlas_wavelength=max_atlas_wavelength,
-            min_intensity=min_intensity,
-            min_distance=min_distance,
-            range_tolerance=self.range_tolerance,
-            vacuum=vacuum,
-            pressure=pressure,
-            temperature=temperature,
-            relative_humidity=relative_humidity,
-        )
-        self.atlas = new_atlas
+        if self.atlas is None:
+
+            new_atlas = Atlas(
+                elements,
+                min_atlas_wavelength=min_atlas_wavelength,
+                max_atlas_wavelength=max_atlas_wavelength,
+                min_intensity=min_intensity,
+                min_distance=min_distance,
+                range_tolerance=self.range_tolerance,
+                vacuum=vacuum,
+                pressure=pressure,
+                temperature=temperature,
+                relative_humidity=relative_humidity,
+            )
+            self.atlas = new_atlas
+
+        else:
+
+            self.atlas.add(
+                elements,
+                min_atlas_wavelength=min_atlas_wavelength,
+                max_atlas_wavelength=max_atlas_wavelength,
+                min_intensity=min_intensity,
+                min_distance=min_distance,
+                vacuum=vacuum,
+                pressure=pressure,
+                temperature=temperature,
+                relative_humidity=relative_humidity,
+            )
+
         self.candidate_tolerance = candidate_tolerance
         self.constrain_poly = constrain_poly
 

src/rascal/plotting.py

@@ -990,6 +990,10 @@ def plot_fit(
 
             spec_max = np.nanmax(spectrum) * 1.05
 
+        else:
+
+            spec_max = vline_max
+
         fitted_peaks = []
         fitted_peaks_adu = []
         fitted_diff = []
@@ -1026,12 +1030,12 @@ def plot_fit(
                     fitted_peaks_adu.append(
                         spectrum[int(calibrator.pix_to_rawpix(p))]
                     )
-                    fitted_diff.append(diff[idx])
-                    calibrator.logger.info(
-                        "- matched to {} A".format(
-                            calibrator.atlas.get_lines()[idx]
-                        )
+                fitted_diff.append(diff[idx])
+                calibrator.logger.info(
+                    "- matched to {} A".format(
+                        calibrator.atlas.get_lines()[idx]
                     )
+                )
 
         x_fitted = calibrator.polyval(fitted_peaks, fit_coeff)
 

test/test_effective_pixel.py

@@ -44,7 +44,7 @@ def test_providing_effective_pixel_not_affecting_fit(mock_show):
         range_tolerance=100.0, min_wavelength=100.0, max_wavelength=1300.0
     )
 
-    c.set_ransac_properties(linear=False, minimum_fit_error=1e-12)
+    c.set_ransac_properties(linear=False, minimum_fit_error=1e-14)
 
     # Add our fake lines as the atlas
     a.add_user_atlas(elements=["Test"] * len(waves), wavelengths=waves)