Various testing spot checks... (#122)

* Drop the draft creation from JOSS on GitHub actions--not needed anymore

* Make unit tests use astropy 5.1 only, per #121

* Numpy version incompatibility check...

* The tests were reading the pip version of muler! that is a fail!

* numpy backwards breaking bug

* numpy compatibiliy deprecation

* Got to try different numpy versions

* another numpy backwards breaking change

* same for nirspec

* Astropy 5.1 has a numpy conflict, apparently?

* Force the most recent versions after all

.github/workflows/muler-tests.yml

@@ -4,14 +4,14 @@ on: [push]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9]
-        specutils-version: [1.5, 1.6, 1.7]
-        astropy-version: [4.3, 5.0]
+        python-version: [3.9]
+        specutils-version: [1.5, 1.9.1]
+        astropy-version: [5.2]
+        numpy-version: [1.18, 1.24]
 
     steps:
       - uses: actions/checkout@v2
@@ -27,8 +27,8 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install flake8 pytest
-          if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
-          pip install astropy==${{ matrix.astropy-version }} specutils==${{ matrix.specutils-version }} 
+          if [ -f docs/requirements_actions.txt ]; then pip install -r docs/requirements_actions.txt; fi
+          pip install astropy==${{ matrix.astropy-version }} specutils==${{ matrix.specutils-version }}
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
@@ -41,4 +41,4 @@ jobs:
           python -c "import sys; print('Python version: ', sys.version)"
           python -c "import specutils; print('specutils version: ', specutils.__version__)"
           python -c "import astropy; print('astropy version: ', astropy.__version__)"
-          pytest -vs
+          pytest -vs

docs/requirements_actions.txt

@@ -0,0 +1,18 @@
+sphinx>=3.2.1
+sphinx-material
+scipy
+pandas
+nbsphinx
+gwcs
+celerite2
+matplotlib
+requests
+ipykernel
+importlib_resources
+h5py
+celerite2
+tqdm
+bokeh # needed for gollum to install on RTD
+gollum==0.2.1
+numpydoc
+sphinx-gallery

environment.yml

@@ -3,16 +3,15 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - python=3.8
+  - python=3.9
   - numpy
   - scipy
   - matplotlib
-  - astropy<5.0
+  - astropy=5.2
   - astroquery
-  - specutils>=1.2
   - tqdm
-  - gwcs<0.17
-  - ndcube<2.0
+  - gwcs
+  - ndcube
   - pandas
   - bokeh
   - jupyter
@@ -35,3 +34,4 @@ dependencies:
   - pip:
       - sphinx-material
       - celerite2
+      - specutils==1.9.1

setup.py

@@ -12,18 +12,18 @@
 
 setuptools.setup(
     name="muler",
-    version="0.3.4",
+    version="0.4.0",
     author="gully",
     author_email="[email protected]",
-    description="A Python package for working with data from IGRINS and HPF",
+    description="A Python package for working with data from various echelle spectrographs",
     long_description=readme,
     long_description_content_type="text/markdown",
     url="https://github.com/OttoStruve/muler",
     install_requires=[
         "numpy",
         "scipy",
-        "astropy>=4.1",
-        "specutils>=1.5",
+        "astropy>=5.2",
+        "specutils>=1.9",
         "pandas",
         "importlib_resources",
         "matplotlib",

src/muler/echelle.py

@@ -538,7 +538,7 @@ def neg_log_like(params, gp):
             spectral_axis=self.wavelength.value * self.wavelength.unit,
             flux=mean_model * self.flux.unit,
             uncertainty=None,
-            mask=np.zeros_like(mean_model, dtype=np.bool),
+            mask=np.zeros_like(mean_model, dtype=bool),
             meta=copy.deepcopy(self.meta),
             wcs=None,
         )

src/muler/hpf.py

@@ -93,14 +93,14 @@ def __init__(self, *args, file=None, order=19, cached_hdus=None, **kwargs):
             hdr = hdus[0].header
 
             ## Target Spectrum
-            lamb = hdus[7].data[order].astype(np.float64) * u.AA
-            flux = hdus[1].data[order].astype(np.float64) * u.ct
-            unc = hdus[4].data[order].astype(np.float64) * u.ct
+            lamb = hdus[7].data[order].astype(float) * u.AA
+            flux = hdus[1].data[order].astype(float) * u.ct
+            unc = hdus[4].data[order].astype(float) * u.ct
             if pipeline == "HPF":
                 unc = np.sqrt(unc.value) * u.ct
 
             meta_dict = {
-                "x_values": np.arange(0, 2048, 1, dtype=np.int),
+                "x_values": np.arange(0, 2048, 1, dtype=int),
                 "pipeline": pipeline,
                 "m": grating_order,
                 "header": hdr,
@@ -122,9 +122,9 @@ def __init__(self, *args, file=None, order=19, cached_hdus=None, **kwargs):
             )
 
             ## Sky Spectrum
-            lamb = hdus[8].data[order].astype(np.float64) * u.AA
-            flux = hdus[2].data[order].astype(np.float64) * u.ct
-            unc = hdus[5].data[order].astype(np.float64) * u.ct
+            lamb = hdus[8].data[order].astype(float) * u.AA
+            flux = hdus[2].data[order].astype(float) * u.ct
+            unc = hdus[5].data[order].astype(float) * u.ct
             if pipeline == "HPF":
                 unc = np.sqrt(unc.value) * u.ct
             uncertainty = StdDevUncertainty(unc)
@@ -142,9 +142,9 @@ def __init__(self, *args, file=None, order=19, cached_hdus=None, **kwargs):
             )
 
             ## LFC Spectrum
-            lamb = hdus[9].data[order].astype(np.float64) * u.AA
-            flux = hdus[3].data[order].astype(np.float64) * u.ct
-            unc = hdus[6].data[order].astype(np.float64) * u.ct
+            lamb = hdus[9].data[order].astype(float) * u.AA
+            flux = hdus[3].data[order].astype(float) * u.ct
+            unc = hdus[6].data[order].astype(float) * u.ct
             if pipeline == "HPF":
                 unc = np.sqrt(unc.value) * u.ct
             uncertainty = StdDevUncertainty(unc)

src/muler/igrins.py

@@ -82,7 +82,7 @@ def __init__(
             if cached_hdus is not None:
                 hdus = cached_hdus[0]
                 if "rtell" in file:
-                    sn = hdus['SNR'].data[order]
+                    sn = hdus["SNR"].data[order]
                     sn_hdus = None
                 else:
                     sn_hdus = cached_hdus[1]
@@ -99,7 +99,7 @@ def __init__(
                         wave_hdus = fits.open(wavefile)
                 else:
                     hdus = fits.open(str(file))
-                    sn = hdus['SNR'].data[order]
+                    sn = hdus["SNR"].data[order]
                     sn_hdus = None
                     if wavefile is not None:
                         wave_hdus = fits.open(wavefile)
@@ -110,13 +110,13 @@ def __init__(
                     "You have passed in a wavefile and a spec_a0v format file, which has its own wavelength solution.  Ignoring the wavefile."
                 )
             elif ".spec_a0v.fits" in file:
-                lamb = hdus["WAVELENGTH"].data[order].astype(np.float64) * u.micron
-                flux = hdus["SPEC_DIVIDE_A0V"].data[order].astype(np.float64) * u.ct
+                lamb = hdus["WAVELENGTH"].data[order].astype(float) * u.micron
+                flux = hdus["SPEC_DIVIDE_A0V"].data[order].astype(float) * u.ct
             elif ("spec.fits" in file) and (wavefile is not None):
                 lamb = (
-                    wave_hdus[0].data[order].astype(np.float64) * 1e-3 * u.micron
+                    wave_hdus[0].data[order].astype(float) * 1e-3 * u.micron
                 )  # Note .wave.fits and .wavesol_v1.fts files store their wavelenghts in nm so they need to be converted to microns
-                flux = hdus[0].data[order].astype(np.float64) * u.ct
+                flux = hdus[0].data[order].astype(float) * u.ct
             elif ("spec.fits" in file) and (wavefile is None):
                 raise Exception(
                     "wavefile must be specified when passing in spec.fits files, which do not come with an in-built wavelength solution."
@@ -128,7 +128,7 @@ def __init__(
                     + " is the wrong file type.  It must be either .spec_a0v.fits or .spec.fits."
                 )
             meta_dict = {
-                "x_values": np.arange(0, 2048, 1, dtype=np.int),
+                "x_values": np.arange(0, 2048, 1, dtype=int),
                 "m": grating_order,
                 "header": hdr,
             }
@@ -214,7 +214,7 @@ def read(file, precache_hdus=True, wavefile=None):
         wavefile : (str)
 
         """
-        #still works
+        # still works
         assert (".spec_a0v.fits" in file) or (".spec.fits" in file)
         hdus = fits.open(file, memmap=False)
         if ".spec_a0v.fits" in file:

src/muler/nirspec.py

@@ -75,9 +75,9 @@ def __init__(self, *args, file=None, order=63, **kwargs):
             hdu0 = hdu[1]
 
             ## Target Spectrum
-            lamb = hdu0.data["wave (A)"].astype(np.float64) * u.AA
-            flux = hdu0.data["flux (cnts)"].astype(np.float64) * u.ct
-            unc = hdu0.data["noise (cnts)"].astype(np.float64) * u.ct
+            lamb = hdu0.data["wave (A)"].astype(float) * u.AA
+            flux = hdu0.data["flux (cnts)"].astype(float) * u.ct
+            unc = hdu0.data["noise (cnts)"].astype(float) * u.ct
 
             uncertainty = StdDevUncertainty(unc)
             mask = np.array(
@@ -100,7 +100,7 @@ def __init__(self, *args, file=None, order=63, **kwargs):
                 hdr = None
 
             meta_dict = {
-                "x_values": hdu0.data["col"].astype(np.int),
+                "x_values": hdu0.data["col"].astype(int),
                 "pipeline": pipeline,
                 "m": grating_order,
                 "header": hdr,
@@ -117,7 +117,7 @@ def __init__(self, *args, file=None, order=63, **kwargs):
             )
 
             ## Sky Spectrum
-            flux = hdu0.data["sky (cnts)"].astype(np.float64) * u.ct
+            flux = hdu0.data["sky (cnts)"].astype(float) * u.ct
 
             sky_spectrum = KeckNIRSPECSpectrum(
                 spectral_axis=lamb,