Merge pull request #89 from jveitchmichaelis/dev-0.3.X

main catching up to v0.3.9
jveitchmichaelis · Mar 25, 2023 · cdc1bf5 · cdc1bf5
2 parents cec48f2 + d82a640
commit cdc1bf5
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,14 +1,14 @@
 repos:
 -   repo: https://github.com/psf/black
-    rev: 22.1.0
+    rev: 23.1.0
     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
@@ -22,3 +22,21 @@ repos:
     # Python checks
     - id: debug-statements
     - id: requirements-txt-fixer
+
+-   repo: local
+    hooks:
+    - id: remarklint
+      name: remarklint
+      language: node
+      entry: remark
+      types: [markdown]
+      args: ["--frail", "--quiet"]
+      additional_dependencies:
+        [
+          remark,
+          remark-lint,
+          remark-cli,
+          remark-preset-lint-recommended,
+          remark-lint-list-item-indent,
+          remark-lint-no-undefined-references,
+        ]
diff --git a/CHANGELOG.rst b/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
 -------------

diff --git a/README.md b/README.md
@@ -1,7 +1,8 @@
 # Rascal: RANSAC Assisted Spectral CALibration
+
 [![Python package](https://github.com/jveitchmichaelis/rascal/actions/workflows/python-package.yml/badge.svg)](https://github.com/jveitchmichaelis/rascal/actions/workflows/python-package.yml)
 [![Coverage Status](https://coveralls.io/repos/github/jveitchmichaelis/rascal/badge.svg?branch=main)](https://coveralls.io/github/jveitchmichaelis/rascal?branch=main)
-[![Readthedocs Status](https://readthedocs.org/projects/rascal/badge/?version=latest&style=flat)](https://rascal.readthedocs.io/en/latest/)
+[![Readthedocs Status](https://readthedocs.org/projects/rascal/badge/?version=latest\&style=flat)](https://rascal.readthedocs.io/en/latest/)
 [![PyPI version](https://badge.fury.io/py/rascal.svg)](https://badge.fury.io/py/rascal)
 [![Downloads](https://pepy.tech/badge/rascal/month)](https://pepy.tech/project/rascal)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4117514.svg)](https://doi.org/10.5281/zenodo.4117514)
@@ -13,43 +14,48 @@ Given a set of peaks located in your spectrum, Rascal will attempt to determine
 
 Unlike other calibration methods, rascal does not require you to manually select lines in your spectrum. Ideally you should know  approximate parameters about your system, namely:
 
-* What arc lamp was used (e.g. Xe, Hg, Ar, CuNeAr)
-* What the dispersion of your spectrometer is (i.e. angstroms/pixel)
-* The spectral range of your system, and the starting wavelength
+*   What arc lamp was used (e.g. Xe, Hg, Ar, CuNeAr)
+*   What the dispersion of your spectrometer is (i.e. angstroms/pixel)
+*   The spectral range of your system, and the starting wavelength
 
 You don't need to know the dispersion and start wavelength exactly. Often this information is provided by the observatory, but if you don't know it, you can take a rough guess. The closer you are to the actual system settings, the more likely it is that Rascal will be able to solve the calibration. Blind calibration, where no parameters are known, is possible but challenging currently. If you don't know the lamp, you can try iterating over the various combinations of sources. Generally when you do get a correct fit, with most astronomical instruments the errors will be extremely low.
 
 More background information can be referred to this [arXiv article](https://ui.adsabs.harvard.edu/abs/2019arXiv191205883V/abstract).
 
-
 ## 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
+
+*   [plotly](https://github.com/plotly/plotly.py) >= 4.0
 
 ## Installation
+
 Instructions can be found [here](https://rascal.readthedocs.io/en/latest/installation/installation.html).
 
 ## Reporting issues/feature requests
+
 Please use the [issue tracker](https://github.com/jveitchmichaelis/rascal/issues) to report any issues or support questions.
 
 ## Getting started
+
 The [quickstart guide](https://rascal.readthedocs.io/en/latest/tutorial/quickstart.html) will show you how to reduce the example dataset.
 
 ## Contributing Code/Documentation
+
 If you are interested in contributing code to the project, thank you! For those unfamiliar with the process of contributing to an open-source project, you may want to read through Github’s own short informational section on how to submit a [contribution](https://opensource.guide/how-to-contribute/#how-to-submit-a-contribution) or send me a message.
 
 Style -- we now use black for formatting, you can easily set this up using a pre-commit hook.
 
-```
-pip install pre-commit
-pre-commit install
-```
+    pip install pre-commit
+    pre-commit install
 
 ## Disclaimer
+
 We duplicate some of the relevant metadata, but we do not process the raw metadata. Some of the metadata this software creates contain full path to the files in your system, which most likely includes a user name on your machine. Please be advised it is your responsibility to be compliant with the privacy law(s) that you are oblidged to follow, and it is your responsibility to remove any metadata that may reveal personal information and/or provide information that can reveal any computing vulunerability.
diff --git a/requirements.txt b/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
diff --git a/setup.cfg b/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

diff --git a/src/rascal/atlas.py b/src/rascal/atlas.py
@@ -152,39 +152,32 @@ def add(
         """
 
         if min_atlas_wavelength is None:
-
             min_atlas_wavelength = (
                 self.min_atlas_wavelength - self.range_tolerance
             )
 
         if max_atlas_wavelength is None:
-
             max_atlas_wavelength = (
                 self.max_atlas_wavelength + self.range_tolerance
             )
 
         if not np.isfinite(min_atlas_wavelength):
-
             raise ValueError(
                 "min_atlas_wavelength has to be finite or None. "
                 "{} is given.".format(min_atlas_wavelength)
             )
 
         if not np.isfinite(max_atlas_wavelength):
-
             raise ValueError(
                 "max_atlas_wavelength has to be finite or None. "
                 "{} is given.".format(max_atlas_wavelength)
             )
 
         if isinstance(elements, str):
-
             elements = [elements]
 
         if elements is not None:
-
             for element in elements:
-
                 (
                     atlas_elements_tmp,
                     atlas_tmp,
@@ -254,21 +247,16 @@ def add_user_atlas(
         """
 
         if not isinstance(elements, list):
-
             elements = list(elements)
 
         if not isinstance(wavelengths, list):
-
             wavelengths = list(wavelengths)
 
         if intensities is None:
-
             intensities = [0] * len(wavelengths)
 
         else:
-
             if not isinstance(intensities, list):
-
                 intensities = list(intensities)
 
         assert len(elements) == len(wavelengths), ValueError(
@@ -279,7 +267,6 @@ def add_user_atlas(
         )
 
         if vacuum:
-
             wavelengths = vacuum_to_air_wavelength(
                 wavelengths, temperature, pressure, relative_humidity
             )
@@ -338,9 +325,7 @@ def remove_atlas_lines_range(self, wavelength, tolerance=10):
         """
 
         for atlas_line in self.atlas_lines:
-
             if abs(atlas_line.wavelength - wavelength) < tolerance:
-
                 self.atlas_lines.remove(atlas_line)
 
     def list(self):
@@ -350,7 +335,6 @@ def list(self):
         """
 
         for line in self.atlas_lines:
-
             print(
                 "Element "
                 + str(line.element)