From c8599e778acde596eeef3f9f14dc934803f01155 Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Wed, 14 Feb 2024 14:04:40 -0500
Subject: [PATCH 01/21] updating install docs to make them simpler and faster

---
 docs/example.rst | 13 -----------
 docs/install.rst | 57 ++++++++++++------------------------------------
 2 files changed, 14 insertions(+), 56 deletions(-)

diff --git a/docs/example.rst b/docs/example.rst
index a176f08c8..bc23a35f3 100644
--- a/docs/example.rst
+++ b/docs/example.rst
@@ -16,19 +16,6 @@ This example is based on a small amount of METAL program data.
 METAL is an HST program (PI: J. Roman-Duval) that included parallel imaging
 of regions in the Large Magellanic Cloud.
 
-If you installed Python through AstroConda, first activate the correct
-AstroConda environment
-
-.. code-block:: console
-
-    $ conda activate astroconda
-
-Verify that the current default Python is version 3
-
-.. code-block:: console
-
-    $ python --version
-
 Next, bring up the BEAST help message, which describes the available switch
 options, with
 
diff --git a/docs/install.rst b/docs/install.rst
index 9b1ff678e..f83f4ad70 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -7,18 +7,7 @@ Requirements
 
 Running the BEAST requires:
 
-- Python >= 3.7
-- Astropy >= 1.3
-
-In turn, Astropy depends on
-`other packages <http://docs.astropy.org/en/latest/install.html>`_ for
-optional features. From these you will need:
-
-- `hdf5 <http://h5py.org/>`_ to read/write `Table` objects from/to HDF5 files.
-
-You will also need:
-
-- `PyTables <http://www.pytables.org/>`_ to manage large amounts of data.
+- Python >= 3.8
 
 One easy way to obtain the above is through the AstroConda Python stack:
 
@@ -27,33 +16,19 @@ One easy way to obtain the above is through the AstroConda Python stack:
   you can use the `conda` command to install any other packages and create
   environments, etc.
 
-- Setup the AstroConda Channel
-
-.. code-block:: console
-
-    $ conda config --add channels http://ssb.stsci.edu/astroconda
-
-- Install AstroConda with Python 3 (recommended)
+- Create a conda environment for the BEAST.
+Replace <env_name> with the name of the conda environment you want (e.g., `beast`).
+The specific version of python can be different than 3.11, note it must be at least 3.8.
 
 .. code-block:: console
 
-    $ conda create -n astroconda stsci
+    $ conda create -n <env_name> python=3.11
 
-- Ensure the minimum Python requirements above are met. If needed, specify the minimum version required
+- Switch to this newly create conda environment
 
 .. code-block:: console
 
-    $ python --version
-    $ conda create -n astroconda stsci python=3.7
-
-- Make sure that the ``PyTables`` and ``hdf5`` packages are installed
-
-.. code-block:: console
-
-    $ conda install -n astroconda pytables
-
-    $ conda install -n astroconda hdf5
-
+    $ conda activate <env_name>
 
 Installation for Users
 ======================
@@ -61,13 +36,10 @@ Installation for Users
 In addition to installing the code, library files also need to be installed.
 See :ref:`library-files`.
 
-.. note::
-   The ``numpy`` package must be installed before installing the BEAST. This package is needed as part of the installation process, not just as a prerequisite for running the BEAST.
-
 Using pip
 ---------
 
-``beast`` can be installed using pip:
+``beast`` can be installed using pip.  This installs the latest released version.
 
 .. code-block:: console
 
@@ -79,7 +51,7 @@ If you already have an older version installed, use:
 
     $ pip install --upgrade beast
 
-Or, from the master trunk on the repository, considered developmental code:
+Or, from the repository directly.  This installs the development version with the latest features.
 
 .. code-block:: console
 
@@ -147,14 +119,13 @@ Installation for Production Runs
 Using a dedicated conda environment for production BEAST runs may be
 desirable. Such an environment provides a way to ensure that
 production runs are reproducible by fixing the versions of all the
-software used. The instructions below assume that the `astroconda channel
-<https://astroconda.readthedocs.io/>`_ is being used.
+software used.
 
 Create a conda environment, and name it differently from your default and other environments:
 
   .. code-block:: console
 
-    $ conda create -n beast_production python=3.6
+    $ conda create -n beast_production python=3.11
 
 Activate the environment after all the packages are finished installing:
 
@@ -170,17 +141,17 @@ Install dependencies using conda (better for speed):
 
 Next, install the BEAST. You have three options:
 
-Option 1: Use pip to install a stable version of the BEAST (e.g. v1.3):
+Option 1: Use pip to install a stable version of the BEAST (e.g. v2.0):
 
   .. code-block:: console
 
-    $ pip install beast==1.3
+    $ pip install beast==2.0
 
 Option 2: Get the latest production branch, which can be ahead of the pypi version:
 
   .. code-block:: console
 
-    $ pip install git+https://github.com/BEAST-Fitting/beast.git@v1.x
+    $ pip install git+https://github.com/BEAST-Fitting/beast.git@v2.x
 
 Option 3: If you'll be doing development, follow the instructions above (:ref:`Dev_install`). Note that you can make separate environments for development and production modes.
 

From fbab10e810000be42e73b1f4904a5d888f029c63 Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Wed, 14 Feb 2024 14:26:34 -0500
Subject: [PATCH 02/21] fixing deprecated pytest behavior

---
 beast/tools/tests/test_verify_beast_settings.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/beast/tools/tests/test_verify_beast_settings.py b/beast/tools/tests/test_verify_beast_settings.py
index 2e5fccf56..75f8fc2bf 100644
--- a/beast/tools/tests/test_verify_beast_settings.py
+++ b/beast/tools/tests/test_verify_beast_settings.py
@@ -1,4 +1,5 @@
 import pytest
+import warnings
 from beast.physicsmodel.stars import isochrone
 from beast.tools import verify_beast_settings
 
@@ -36,7 +37,8 @@ class settings_mock_allowwarn(settings_mock_nofA):
 
 def test_verifyparams_nowarning():
     """Test: verify_beast_settings for case of no warnings or exceptions."""
-    with pytest.warns(None) as record:
+    # with pytest.warns(None) as record:
+    with warnings.catch_warnings(record=True) as record:
         verify_beast_settings.verify_input_format(settings_mock())
     assert len(record) == 0
 

From c09fbc185bac06470c36809fa2767afd2cd7e277 Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Wed, 14 Feb 2024 14:47:55 -0500
Subject: [PATCH 03/21] formating issue

---
 docs/install.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/install.rst b/docs/install.rst
index f83f4ad70..a8fb2782f 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -17,8 +17,8 @@ One easy way to obtain the above is through the AstroConda Python stack:
   environments, etc.
 
 - Create a conda environment for the BEAST.
-Replace <env_name> with the name of the conda environment you want (e.g., `beast`).
-The specific version of python can be different than 3.11, note it must be at least 3.8.
+  Replace <env_name> with the name of the conda environment you want (e.g., `beast`).
+  The specific version of python can be different than 3.11, note it must be at least 3.8.
 
 .. code-block:: console
 

From 7b0cb9fdd063a7cd2ac92b8c55006d9fc38016f9 Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Wed, 14 Feb 2024 15:37:38 -0500
Subject: [PATCH 04/21] adding in ACS HRC filters and enhancing the filter
 plotting routine

---
 beast/plotting/plot_filters.py | 32 +++++++++++++++-------
 beast/tools/make_libfile.py    | 50 +++++++++++++++++++++++++++++++++-
 2 files changed, 71 insertions(+), 11 deletions(-)

diff --git a/beast/plotting/plot_filters.py b/beast/plotting/plot_filters.py
index 06bd81bda..394ede3db 100755
--- a/beast/plotting/plot_filters.py
+++ b/beast/plotting/plot_filters.py
@@ -16,7 +16,7 @@ def plot_filters(
     filter_names,
     filterLib=None,
     save_name="beast_filters",
-    xlim=[1.4e3, 2e4],
+    xlim=[3e3, 1e3],
     ylim=[1e-4, 2],
     show_plot=True,
 ):
@@ -50,8 +50,11 @@ def plot_filters(
     )
 
     color_indices = np.log10(np.array(np.sort([f.norm for f in flist])))
-    color_indices -= color_indices.min()
-    color_indices /= color_indices.max()
+    if len(color_indices) > 1:
+        color_indices -= color_indices.min()
+        color_indices /= color_indices.max()
+    else:
+        color_indices = [0.0]
 
     cmap = mpl.cm.plasma
     # ax.set_prop_cycle(color=[cmap(i) for i in color_indices])
@@ -61,19 +64,25 @@ def plot_filters(
         c = next(color)
         ax.plot(f.wavelength, f.transmit, color=c, lw=2)
         ax.fill_between(f.wavelength, f.transmit, alpha=0.2, color=c)
+        yval_text = max(f.transmit * 0.1)
         ax.text(
-            np.nanmean(f.wavelength[f.transmit > 100.0 * ylim[0]]),
-            1.3 * np.nanmax(f.transmit[f.transmit > ylim[0]]),
+            np.nanmean(f.wavelength[f.transmit > yval_text]),
+            1.3 * np.nanmax(f.transmit[f.transmit > yval_text]),
             f.name.split("_")[-1],
             ha="center",
             color=c,
         )
+        gvals = (f.transmit > ylim[0]) & (f.transmit < ylim[1])
+        if min(f.wavelength[gvals]) < xlim[0]:
+            xlim[0] = min(f.wavelength[gvals])
+        if max(f.wavelength[gvals]) > xlim[1]:
+            xlim[1] = max(f.wavelength[gvals])
 
     ax.set_xscale("log")
     ax.set_yscale("log")
     ax.set_xlim(xlim)
     ax.set_ylim(ylim)
-    ax.set_xlabel(r"$\lambda$ [$\mu m$]")
+    ax.set_xlabel(r"$\lambda$ [$\AA$]")
     ax.set_ylabel(r"$B_i(\lambda)$")
 
     # ax.set_xticks([0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 2.0])
@@ -95,9 +104,7 @@ def plot_filters(
         default="filters.appendVegaFilter",
         help="Save figure to file",
     )
-    args = parser.parse_args()
-
-    filter_names = [
+    def_filter_names = [
         "HST_WFC3_F225W",
         "HST_WFC3_F275W",
         "HST_WFC3_F336W",
@@ -107,8 +114,13 @@ def plot_filters(
         "HST_WFC3_F110W",
         "HST_WFC3_F160W",
     ]
+    parser.add_argument("filter_names",
+                        help="names of filters",
+                        nargs='+',
+                        default=def_filter_names)
+    args = parser.parse_args()
 
-    fig = plot_filters(filter_names, show_plot=False)
+    fig = plot_filters(args.filter_names, show_plot=False)
 
     if args.tex:
         plt.rc({"usetex": True})
diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index 1a083e937..dccc6966c 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -84,6 +84,16 @@ def make_libfile():
         "f775w",
         "f814w",
     ]
+
+    acs_hrc = [
+        "f115lp",
+        "f125lp",
+        "f140lp",
+        "f150lp",
+        "f165lp",
+        "f122m",
+    ]
+
     # galex
     galex = ["fuv", "nuv"]
 
@@ -228,7 +238,7 @@ def make_libfile():
         pwaves.append(newfilt.lpivot.value)
         comments.append("avg of 1, 2, 3, 4")
 
-    # Loop through ACS filters
+    # Loop through ACS WFC filters
     for filt in acs_wfc:
 
         # define wfc1, wfc2 modes
@@ -270,6 +280,44 @@ def make_libfile():
         pwaves.append(newfilt.lpivot.value)
         comments.append("avg of wfc1 and wfc2")
 
+    # Loop through ACS HRC filters
+    for filt in acs_hrc:
+
+        # define ir mode
+        mode = "acs, sbc, " + filt
+
+        # pull bandpasses from stsynphot for the two uvis modes
+        bp = stsyn.band(mode)
+
+        # extract the wavelength array
+        wave = bp.waveset
+
+        # define the filter name
+        filter_name = "HST_ACS_SBC_" + filt.upper()
+
+        # build array of wavelength and throughput
+        arr = np.array(
+            list(zip(wave.value.astype(np.float64), bp(wave).astype(np.float64))),
+            dtype=[("WAVELENGTH", "float64"), ("THROUGHPUT", "float64")],
+        )
+
+        # append dataset to the hdf5 filters group
+        f.create_dataset(filter_name, data=arr)
+
+        # generate filter instance to compute relevant info
+        newfilt = phot.Filter(wave, bp(wave), name=filt.upper())
+
+        # populate contents lists with relevant information
+        tablenames.append(filter_name)
+        observatories.append("HST")
+        instruments.append("ACS")
+        names.append(newfilt.name)
+        norms.append(newfilt.norm.value)
+        cwaves.append(newfilt.cl.value)
+        pwaves.append(newfilt.lpivot.value)
+        comments.append("")
+
+
     # Loop through GALEX filters:
     for filt in galex:
         # define ir mode

From 0479948d28422c09a3647d928440433cfb7b26f5 Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Wed, 14 Feb 2024 15:42:23 -0500
Subject: [PATCH 05/21] update variables to match reality

---
 beast/tools/make_libfile.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index dccc6966c..981204a4d 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -85,7 +85,7 @@ def make_libfile():
         "f814w",
     ]
 
-    acs_hrc = [
+    acs_sbc = [
         "f115lp",
         "f125lp",
         "f140lp",
@@ -280,8 +280,8 @@ def make_libfile():
         pwaves.append(newfilt.lpivot.value)
         comments.append("avg of wfc1 and wfc2")
 
-    # Loop through ACS HRC filters
-    for filt in acs_hrc:
+    # Loop through ACS SBC filters
+    for filt in acs_sbc:
 
         # define ir mode
         mode = "acs, sbc, " + filt

From 7f05a535d325d45b5a290d6e1365a0df52c48dcd Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Wed, 14 Feb 2024 15:44:08 -0500
Subject: [PATCH 06/21] fix codestyle

---
 beast/tools/make_libfile.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index 981204a4d..26ff42d74 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -317,7 +317,6 @@ def make_libfile():
         pwaves.append(newfilt.lpivot.value)
         comments.append("")
 
-
     # Loop through GALEX filters:
     for filt in galex:
         # define ir mode

From bfd062461f5d5d3af298e0abdb4abcc60f33e484 Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Thu, 15 Feb 2024 10:05:28 -0500
Subject: [PATCH 07/21] adding in MIRI filters

---
 beast/plotting/plot_filters.py | 17 ++++---
 beast/tools/make_libfile.py    | 90 ++++++++++++++++++++++++++++++++++
 2 files changed, 101 insertions(+), 6 deletions(-)

diff --git a/beast/plotting/plot_filters.py b/beast/plotting/plot_filters.py
index 394ede3db..1d093d517 100755
--- a/beast/plotting/plot_filters.py
+++ b/beast/plotting/plot_filters.py
@@ -16,7 +16,7 @@ def plot_filters(
     filter_names,
     filterLib=None,
     save_name="beast_filters",
-    xlim=[3e3, 1e3],
+    xlim=None,
     ylim=[1e-4, 2],
     show_plot=True,
 ):
@@ -42,7 +42,8 @@ def plot_filters(
     fig, ax = plt.subplots(1, 1, figsize=(10, 6))
 
     # wavelength grid in angstroms for response functions
-    waves = np.logspace(3, np.log10(3e4), 501)
+    #  cover all HST and JWST wavelengths
+    waves = np.logspace(np.log10(912.), np.log10(3e5), 1001)
 
     # read in the filter response functions
     flist = phot.load_filters(
@@ -60,6 +61,7 @@ def plot_filters(
     # ax.set_prop_cycle(color=[cmap(i) for i in color_indices])
     color = iter(cmap(np.linspace(0.2, 0.8, len(filter_names))))
 
+    dxlim = [3e5, 912.]
     for f in flist:
         c = next(color)
         ax.plot(f.wavelength, f.transmit, color=c, lw=2)
@@ -73,10 +75,13 @@ def plot_filters(
             color=c,
         )
         gvals = (f.transmit > ylim[0]) & (f.transmit < ylim[1])
-        if min(f.wavelength[gvals]) < xlim[0]:
-            xlim[0] = min(f.wavelength[gvals])
-        if max(f.wavelength[gvals]) > xlim[1]:
-            xlim[1] = max(f.wavelength[gvals])
+        if min(f.wavelength[gvals]) < dxlim[0]:
+            dxlim[0] = min(f.wavelength[gvals])
+        if max(f.wavelength[gvals]) > dxlim[1]:
+            dxlim[1] = max(f.wavelength[gvals])
+
+    if xlim is None:
+        xlim = dxlim
 
     ax.set_xscale("log")
     ax.set_yscale("log")
diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index 26ff42d74..38e71b473 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -2,6 +2,8 @@
 import numpy as np
 
 import stsynphot as stsyn
+from pandeia.engine.instrument_factory import InstrumentFactory
+import astropy.units as u
 
 import h5py
 
@@ -18,23 +20,39 @@ def make_libfile():
         "f218w",
         "f225w",
         "f275w",
+        "f280n",
         "f336w",
+        "f343n",
+        "f373n",
         "f390m",
         "f390w",
+        "f395n",
         "f410m",
         "f438w",
         "f467m",
+        "f469n",
         "f475w",
+        "f487n",
+        "f502n",
         "f547m",
         "f555w",
         "f606w",
         "f621m",
         "f625w",
+        "f631n",
+        "f645n",
+        "f656n",
+        "f657n",
+        "f658n",
+        "f665n",
+        "f673n",
+        "f680n",
         "f689m",
         "f763m",
         "f775w",
         "f814w",
         "f845m",
+        "f953n",
     ]
 
     wfc3_ir = [
@@ -94,6 +112,22 @@ def make_libfile():
         "f122m",
     ]
 
+    jwst_miri = [
+        "f560w",
+        "f770w",
+        "f1000w",
+        "f1065c",
+        "f1140c",
+        "f1130w",
+        "f1280w",
+        "f1500w",
+        "f1550c",
+        "f1800w",
+        "f2100w",
+        "f2300c",
+        "f2550w",
+    ]
+
     # galex
     galex = ["fuv", "nuv"]
 
@@ -353,6 +387,62 @@ def make_libfile():
         pwaves.append(newfilt.lpivot.value)
         comments.append("")
 
+    for filt in jwst_miri:
+        # mock configuration
+        conf = {
+            "detector": {
+                "nexp": 1,
+                "ngroup": 10,
+                "nint": 1,
+                "readout_pattern": "fastr1",
+                "subarray": "full",
+            },
+            "dynamic_scene": True,
+            "instrument": {
+                "aperture": "imager",
+                "filter": filt,
+                "instrument": "miri",
+                "mode": "imaging",
+            },
+        }
+
+        # create a configured instrument
+        instrument_factory = InstrumentFactory(config=conf)
+
+        # set up your wavelengths
+        pwave = np.logspace(np.log10(3.0), np.log10(40.0), 501) * u.micron
+
+        # get the throughput of the instrument over the desired wavelength range
+        eff = instrument_factory.get_total_eff(pwave.value)
+
+        # get wavelengths in Angstroms
+        wave = pwave.to(u.AA)
+
+        # define the filter name
+        filter_name = "JWST_MIRI_" + filt.upper()
+
+        # build array of wavelength and throughput
+        arr = np.array(
+            list(zip(wave.value.astype(np.float64), eff.astype(np.float64))),
+            dtype=[("WAVELENGTH", "float64"), ("THROUGHPUT", "float64")],
+        )
+
+        # append dataset to the hdf5 filters group
+        f.create_dataset(filter_name, data=arr)
+
+        # generate filter instance to compute relevant info
+        newfilt = phot.Filter(wave, eff, name=filt.upper())
+
+        # populate contents lists with relevant information
+        tablenames.append(filter_name)
+        observatories.append("GALEX")
+        instruments.append("GALEX")
+        names.append(newfilt.name)
+        norms.append(newfilt.norm.value)
+        cwaves.append(newfilt.cl.value)
+        pwaves.append(newfilt.lpivot.value)
+        comments.append("")
+
     # smash the contents arrays together
     contents = np.array(
         list(

From 2863b2851022c1244e82561ff23c32c5c408008a Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Thu, 15 Feb 2024 10:25:08 -0500
Subject: [PATCH 08/21] adding in NIRCam filters

---
 beast/tools/make_libfile.py | 146 +++++++++++++++++++++++++++++++-----
 1 file changed, 129 insertions(+), 17 deletions(-)

diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index 38e71b473..ac2ab6605 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -112,21 +112,18 @@ def make_libfile():
         "f122m",
     ]
 
-    jwst_miri = [
-        "f560w",
-        "f770w",
-        "f1000w",
-        "f1065c",
-        "f1140c",
-        "f1130w",
-        "f1280w",
-        "f1500w",
-        "f1550c",
-        "f1800w",
-        "f2100w",
-        "f2300c",
-        "f2550w",
-    ]
+    # fmt: off
+    jwst_nircam_sw = ["f150w2", "f070w", "f090w", "f115w", "f150w", "f200w",
+                      "f140m", "f162m", "f182m", "f210m",
+                      "f164n", "f187n", "f212n"]
+
+    jwst_nircam_lw = ["f332w2", "f277w", "f356w", "f444w",
+                      "f250m", "f300m", "f335m", "f360m", "f410m", "f430m", "f460m", "f480m",
+                      "f323n", "f405n", "f466n", "f470n"]
+
+    jwst_miri = ["f560w", "f770w", "f1000w", "f1130w", "f1280w", "f1500w", "f1800w", "f2100w", "f2550w",
+                 "f1065c", "f1140c", "f1550c", "f2300c"]
+    # fmt: on
 
     # galex
     galex = ["fuv", "nuv"]
@@ -387,6 +384,121 @@ def make_libfile():
         pwaves.append(newfilt.lpivot.value)
         comments.append("")
 
+    for filt in jwst_nircam_sw:
+        # mock configuration
+        conf = {
+            "detector": {
+                "nexp": 1,
+                "ngroup": 10,
+                "nint": 1,
+                "readout_pattern": "deep2",
+                "subarray": "full"
+            },
+            "instrument": {
+                "aperture": "sw",
+                "disperser": "null",
+                "filter": filt,
+                "instrument": "nircam",
+                "mode": "sw_imaging"
+            },
+        }
+
+        # create a configured instrument
+        instrument_factory = InstrumentFactory(config=conf)
+
+        # set up your wavelengths
+        pwave = np.logspace(np.log10(0.5), np.log10(7.0), 501) * u.micron
+
+        # get the throughput of the instrument over the desired wavelength range
+        eff = instrument_factory.get_total_eff(pwave.value)
+
+        # get wavelengths in Angstroms
+        wave = pwave.to(u.AA)
+
+        # define the filter name
+        filter_name = "JWST_NIRCAM_" + filt.upper()
+
+        # build array of wavelength and throughput
+        arr = np.array(
+            list(zip(wave.value.astype(np.float64), eff.astype(np.float64))),
+            dtype=[("WAVELENGTH", "float64"), ("THROUGHPUT", "float64")],
+        )
+
+        # append dataset to the hdf5 filters group
+        f.create_dataset(filter_name, data=arr)
+
+        # generate filter instance to compute relevant info
+        newfilt = phot.Filter(wave, eff, name=filt.upper())
+
+        # populate contents lists with relevant information
+        tablenames.append(filter_name)
+        observatories.append("JWST")
+        instruments.append("NIRCAM")
+        names.append(newfilt.name)
+        norms.append(newfilt.norm.value)
+        cwaves.append(newfilt.cl.value)
+        pwaves.append(newfilt.lpivot.value)
+        comments.append("")
+
+
+    for filt in jwst_nircam_lw:
+        # mock configuration
+        conf = {
+            "detector": {
+                "nexp": 1,
+                "ngroup": 10,
+                "nint": 1,
+                "readout_pattern": "deep2",
+                "subarray": "full"
+            },
+            "instrument": {
+                "aperture": "lw",
+                "disperser": "null",
+                "filter": filt,
+                "instrument": "nircam",
+                "mode": "lw_imaging"
+            },
+        }
+
+        # create a configured instrument
+        instrument_factory = InstrumentFactory(config=conf)
+
+        # set up your wavelengths
+        pwave = np.logspace(np.log10(0.5), np.log10(7.0), 501) * u.micron
+
+        # get the throughput of the instrument over the desired wavelength range
+        eff = instrument_factory.get_total_eff(pwave.value)
+
+        # get wavelengths in Angstroms
+        wave = pwave.to(u.AA)
+
+        # define the filter name
+        filter_name = "JWST_NIRCAM_" + filt.upper()
+
+        # build array of wavelength and throughput
+        arr = np.array(
+            list(zip(wave.value.astype(np.float64), eff.astype(np.float64))),
+            dtype=[("WAVELENGTH", "float64"), ("THROUGHPUT", "float64")],
+        )
+
+        # append dataset to the hdf5 filters group
+        f.create_dataset(filter_name, data=arr)
+
+        # generate filter instance to compute relevant info
+        newfilt = phot.Filter(wave, eff, name=filt.upper())
+
+        # populate contents lists with relevant information
+        tablenames.append(filter_name)
+        observatories.append("JWST")
+        instruments.append("NIRCAM")
+        names.append(newfilt.name)
+        norms.append(newfilt.norm.value)
+        cwaves.append(newfilt.cl.value)
+        pwaves.append(newfilt.lpivot.value)
+        comments.append("")
+
+
+
     for filt in jwst_miri:
         # mock configuration
         conf = {
@@ -435,8 +547,8 @@ def make_libfile():
 
         # populate contents lists with relevant information
         tablenames.append(filter_name)
-        observatories.append("GALEX")
-        instruments.append("GALEX")
+        observatories.append("JWST")
+        instruments.append("MIRI")
         names.append(newfilt.name)
         norms.append(newfilt.norm.value)
         cwaves.append(newfilt.cl.value)

From bca4bc1e5c7aee482a9f6a60432e8bd8a5696761 Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Thu, 15 Feb 2024 10:30:06 -0500
Subject: [PATCH 09/21] adding in NIRISS

---
 beast/tools/make_libfile.py | 57 +++++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)

diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index ac2ab6605..8dad29eef 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -120,6 +120,9 @@ def make_libfile():
     jwst_nircam_lw = ["f332w2", "f277w", "f356w", "f444w",
                       "f250m", "f300m", "f335m", "f360m", "f410m", "f430m", "f460m", "f480m",
                       "f323n", "f405n", "f466n", "f470n"]
+    
+    jwst_niriss = ["f090w", "f115w", "f150w", "f200w", "f277w", "f356w", "f444w",
+                   "f140m", "f158m", "f380m", "f430m", "f480m"]
 
     jwst_miri = ["f560w", "f770w", "f1000w", "f1130w", "f1280w", "f1500w", "f1800w", "f2100w", "f2550w",
                  "f1065c", "f1140c", "f1550c", "f2300c"]
@@ -497,7 +500,61 @@ def make_libfile():
         pwaves.append(newfilt.lpivot.value)
         comments.append("")
 
+    for filt in jwst_niriss:
+        # mock configuration
+        conf = {
+            "detector": {
+                "nexp": 1,
+                "ngroup": 10,
+                "nint": 1,
+                "readout_pattern": "nis",
+                "subarray": "full"
+            },
+            "instrument": {
+                "aperture": "imager",
+                "disperser": "null",
+                "filter": filt,
+                "instrument": "niriss",
+                "mode": "imaging"
+            },
+        }
+
+        # create a configured instrument
+        instrument_factory = InstrumentFactory(config=conf)
+
+        # set up your wavelengths
+        pwave = np.logspace(np.log10(0.5), np.log10(7.0), 501) * u.micron
+
+        # get the throughput of the instrument over the desired wavelength range
+        eff = instrument_factory.get_total_eff(pwave.value)
+
+        # get wavelengths in Angstroms
+        wave = pwave.to(u.AA)
+
+        # define the filter name
+        filter_name = "JWST_NIRISS_" + filt.upper()
+
+        # build array of wavelength and throughput
+        arr = np.array(
+            list(zip(wave.value.astype(np.float64), eff.astype(np.float64))),
+            dtype=[("WAVELENGTH", "float64"), ("THROUGHPUT", "float64")],
+        )
+
+        # append dataset to the hdf5 filters group
+        f.create_dataset(filter_name, data=arr)
+
+        # generate filter instance to compute relevant info
+        newfilt = phot.Filter(wave, eff, name=filt.upper())
 
+        # populate contents lists with relevant information
+        tablenames.append(filter_name)
+        observatories.append("JWST")
+        instruments.append("NIRISS")
+        names.append(newfilt.name)
+        norms.append(newfilt.norm.value)
+        cwaves.append(newfilt.cl.value)
+        pwaves.append(newfilt.lpivot.value)
+        comments.append("")
 
     for filt in jwst_miri:
         # mock configuration

From 6c2c4c015115d21604882cc7d982db0a003fae5c Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Thu, 15 Feb 2024 10:30:29 -0500
Subject: [PATCH 10/21] removing extra space

---
 beast/tools/make_libfile.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index 8dad29eef..60dae6ee4 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -120,7 +120,7 @@ def make_libfile():
     jwst_nircam_lw = ["f332w2", "f277w", "f356w", "f444w",
                       "f250m", "f300m", "f335m", "f360m", "f410m", "f430m", "f460m", "f480m",
                       "f323n", "f405n", "f466n", "f470n"]
-    
+
     jwst_niriss = ["f090w", "f115w", "f150w", "f200w", "f277w", "f356w", "f444w",
                    "f140m", "f158m", "f380m", "f430m", "f480m"]
 

From 8eb6ea2025873678b6b9b100fb3cd9659e07b047 Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Thu, 15 Feb 2024 10:31:10 -0500
Subject: [PATCH 11/21] extra line

---
 beast/tools/make_libfile.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index 60dae6ee4..94e8bda44 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -443,7 +443,6 @@ def make_libfile():
         pwaves.append(newfilt.lpivot.value)
         comments.append("")
 
-
     for filt in jwst_nircam_lw:
         # mock configuration
         conf = {

From 6cd4a5790b45fb82b4c5b74a27b0d6c603ec5159 Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Thu, 15 Feb 2024 11:28:35 -0500
Subject: [PATCH 12/21] adding in a test to make sure filters and vega hdf5
 files are consisent

---
 .../tests/test_filters_and_vega_consistent.py | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 beast/observationmodel/tests/test_filters_and_vega_consistent.py

diff --git a/beast/observationmodel/tests/test_filters_and_vega_consistent.py b/beast/observationmodel/tests/test_filters_and_vega_consistent.py
new file mode 100644
index 000000000..8572899cf
--- /dev/null
+++ b/beast/observationmodel/tests/test_filters_and_vega_consistent.py
@@ -0,0 +1,28 @@
+from astropy.table import QTable
+
+from beast.config import __ROOT__
+from beast.observationmodel.vega import Vega
+from beast.observationmodel import phot
+
+def test_filters_and_vega_consistent():
+    """
+    Test to ensure that the filters.hd5 and vega.hd5 are consistent.
+    In other words, both have the same filters.
+    """
+    ftab = QTable.read(__ROOT__ + "filters.hd5", path="content")
+    vtab = QTable.read(__ROOT__ + "vega.hd5", path="sed")
+
+    otxt = ""
+    for cfilt in ftab["TABLENAME"].data:
+        if cfilt not in vtab["FNAME"].data:
+            otxt = f"{otxt} {cfilt}"
+    assert otxt == "", "filters in filters.hd5 missing from vega.hd5:" + otxt
+
+    otxt = ""
+    for cfilt in vtab["FNAME"].data:
+        if cfilt not in ftab["TABLENAME"].data:
+            otxt = f"{otxt} {cfilt}"
+    assert otxt == "", "filters in vega.hd5 missing from filters.hd5:" + otxt
+
+if __name__ == "__main__":  # pragma: no cover
+    test_filters_and_vega_consistent()
\ No newline at end of file

From e3858927f64a4134629191f7d68e6e5b4d738723 Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Thu, 15 Feb 2024 11:36:39 -0500
Subject: [PATCH 13/21] adding dependancy

---
 setup.cfg | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.cfg b/setup.cfg
index ca16800c7..e42fca74a 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -30,6 +30,7 @@ install_requires =
     graphviz
     asdf
     stsynphot
+    pandeia.engine
 
 [options.entry_points]
 console_scripts =

From cda417fb90e58126a7f5e19b2e1fb000d71ef41c Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Thu, 15 Feb 2024 11:55:10 -0500
Subject: [PATCH 14/21] allow new test to run remotely

---
 .../tests/test_filters_and_vega_consistent.py               | 5 +++++
 beast/tools/get_libfiles.py                                 | 6 ++++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/beast/observationmodel/tests/test_filters_and_vega_consistent.py b/beast/observationmodel/tests/test_filters_and_vega_consistent.py
index 8572899cf..d40d6e5e4 100644
--- a/beast/observationmodel/tests/test_filters_and_vega_consistent.py
+++ b/beast/observationmodel/tests/test_filters_and_vega_consistent.py
@@ -1,6 +1,7 @@
 from astropy.table import QTable
 
 from beast.config import __ROOT__
+from beast.tools import get_libfiles
 from beast.observationmodel.vega import Vega
 from beast.observationmodel import phot
 
@@ -9,6 +10,10 @@ def test_filters_and_vega_consistent():
     Test to ensure that the filters.hd5 and vega.hd5 are consistent.
     In other words, both have the same filters.
     """
+
+    # download the BEAST library files
+    get_libfiles.get_libfiles(vega_filters_only=True)
+
     ftab = QTable.read(__ROOT__ + "filters.hd5", path="content")
     vtab = QTable.read(__ROOT__ + "vega.hd5", path="sed")
 
diff --git a/beast/tools/get_libfiles.py b/beast/tools/get_libfiles.py
index de79a7184..a45559f0b 100644
--- a/beast/tools/get_libfiles.py
+++ b/beast/tools/get_libfiles.py
@@ -15,12 +15,14 @@ def _download_rename(filename, url_loc, local_loc):
     return filename
 
 
-def get_libfiles():
+def get_libfiles(vega_filters_only=False):
     """
     Download all the library files needed by the BEAST
     """
     for ckey, clib in libs.items():
-        _download_rename(clib, libs_server, __ROOT__)
+        if ((not vega_filters_only) or
+            (vega_filters_only & (ckey in ["vega", "filters"]))):
+            _download_rename(clib, libs_server, __ROOT__)
 
 
 if __name__ == "__main__":  # pragma: no cover

From 1ff6dcf9e561a35685f77ad39e4c57da65629eca Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Thu, 15 Feb 2024 11:58:10 -0500
Subject: [PATCH 15/21] fixing codestyle

---
 .../tests/test_filters_and_vega_consistent.py               | 6 +++---
 beast/tools/get_libfiles.py                                 | 3 +--
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/beast/observationmodel/tests/test_filters_and_vega_consistent.py b/beast/observationmodel/tests/test_filters_and_vega_consistent.py
index d40d6e5e4..8578f383c 100644
--- a/beast/observationmodel/tests/test_filters_and_vega_consistent.py
+++ b/beast/observationmodel/tests/test_filters_and_vega_consistent.py
@@ -2,8 +2,7 @@
 
 from beast.config import __ROOT__
 from beast.tools import get_libfiles
-from beast.observationmodel.vega import Vega
-from beast.observationmodel import phot
+
 
 def test_filters_and_vega_consistent():
     """
@@ -29,5 +28,6 @@ def test_filters_and_vega_consistent():
             otxt = f"{otxt} {cfilt}"
     assert otxt == "", "filters in vega.hd5 missing from filters.hd5:" + otxt
 
+
 if __name__ == "__main__":  # pragma: no cover
-    test_filters_and_vega_consistent()
\ No newline at end of file
+    test_filters_and_vega_consistent()
diff --git a/beast/tools/get_libfiles.py b/beast/tools/get_libfiles.py
index a45559f0b..a3372b615 100644
--- a/beast/tools/get_libfiles.py
+++ b/beast/tools/get_libfiles.py
@@ -20,8 +20,7 @@ def get_libfiles(vega_filters_only=False):
     Download all the library files needed by the BEAST
     """
     for ckey, clib in libs.items():
-        if ((not vega_filters_only) or
-            (vega_filters_only & (ckey in ["vega", "filters"]))):
+        if ((not vega_filters_only) or (vega_filters_only & (ckey in ["vega", "filters"]))):
             _download_rename(clib, libs_server, __ROOT__)
 
 

From 7a3fc65bec6a6dc4ef56c7f64cf4cdc248489355 Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Thu, 15 Feb 2024 16:16:16 -0500
Subject: [PATCH 16/21] adding updating of vega.hd5 file

---
 beast/tools/make_libfile.py | 65 +++++++++++++++++++++++++++++++++++--
 1 file changed, 63 insertions(+), 2 deletions(-)

diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index 94e8bda44..23a33c2e0 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -1,9 +1,11 @@
 # script to generate BEAST library files
+import os
 import numpy as np
 
 import stsynphot as stsyn
 from pandeia.engine.instrument_factory import InstrumentFactory
 import astropy.units as u
+from astropy.table import QTable
 
 import h5py
 
@@ -11,7 +13,7 @@
 from beast.observationmodel import phot
 
 
-def make_libfile():
+def make_filters_libfile():
     """
     Extract filters from STSYNPHOT and save to main library file.
     """
@@ -644,5 +646,64 @@ def make_libfile():
     hf.close()
 
 
+def make_vega_libfile():
+
+    # Read an updated filters.hd5 lib
+    __default_filtlist__ = __ROOT__ + "/filters.hd5"
+    filtlist = QTable.read(__default_filtlist__, path="content")
+    filters = [cfilt.decode("UTF-8") for cfilt in filtlist["TABLENAME"].data]
+
+    # filenames for vega info
+    __default_vega__ = __ROOT__ + "/vega.hd5"
+    __default_vega_old__ = __ROOT__ + "/vega_old.hd5"
+
+    # rename the current file so we can write a new version
+    os.rename(__default_vega__, __default_vega_old__)
+
+    # Get a spectrum from the need-to-be updated vega lib
+    vega_old = QTable.read(__default_vega_old__, path="spectrum")
+    vl = vega_old["WAVELENGTH"].data
+    vf = vega_old["FLUX"].data
+
+    # Write out an updated vega.hd5 file
+    vega = h5py.File(__default_vega__, "w")
+
+    vega.create_dataset("spectrum", data=vega_old)
+    flist = phot.load_filters(filters, interp=True, lamb=vl, filterLib=__default_filtlist__)
+
+    fname = []
+    cwave = []
+    lum = []
+    mag = []
+
+    for i in range(len(flist)):
+        fname.append(flist[i].name)
+        cwave.append(flist[i].cl)
+        flux = flist[i].getFlux(vl, vf)
+        lum.append(flux)
+        mag.append(-2.5 * np.log10(flux))
+
+    contents = np.array(
+            list(
+                zip(
+                    fname,
+                    cwave,
+                    lum,
+                    mag,
+                )
+            ),
+            dtype=[
+                ("FNAME", "S30"),
+                ("CWAVE", "<f8"),
+                ("LUM", "<f8"),
+                ("MAG", "<f8"),
+            ],
+        )
+
+    vega.create_dataset("sed", data=contents)
+    vega.close()
+
+
 if __name__ == "__main__":  # pragma: no cover
-    make_libfile()
+    make_filters_libfile()
+    make_vega_libfile()

From 4925595e61f25f4b9a515880f2844201d43aae6d Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Thu, 15 Feb 2024 16:18:57 -0500
Subject: [PATCH 17/21] fixing codestyle

---
 beast/tools/make_libfile.py | 46 +++++++++++++++++++------------------
 1 file changed, 24 insertions(+), 22 deletions(-)

diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index 23a33c2e0..28abe18ea 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -397,14 +397,14 @@ def make_filters_libfile():
                 "ngroup": 10,
                 "nint": 1,
                 "readout_pattern": "deep2",
-                "subarray": "full"
+                "subarray": "full",
             },
             "instrument": {
                 "aperture": "sw",
                 "disperser": "null",
                 "filter": filt,
                 "instrument": "nircam",
-                "mode": "sw_imaging"
+                "mode": "sw_imaging",
             },
         }
 
@@ -453,14 +453,14 @@ def make_filters_libfile():
                 "ngroup": 10,
                 "nint": 1,
                 "readout_pattern": "deep2",
-                "subarray": "full"
+                "subarray": "full",
             },
             "instrument": {
                 "aperture": "lw",
                 "disperser": "null",
                 "filter": filt,
                 "instrument": "nircam",
-                "mode": "lw_imaging"
+                "mode": "lw_imaging",
             },
         }
 
@@ -509,14 +509,14 @@ def make_filters_libfile():
                 "ngroup": 10,
                 "nint": 1,
                 "readout_pattern": "nis",
-                "subarray": "full"
+                "subarray": "full",
             },
             "instrument": {
                 "aperture": "imager",
                 "disperser": "null",
                 "filter": filt,
                 "instrument": "niriss",
-                "mode": "imaging"
+                "mode": "imaging",
             },
         }
 
@@ -669,7 +669,9 @@ def make_vega_libfile():
     vega = h5py.File(__default_vega__, "w")
 
     vega.create_dataset("spectrum", data=vega_old)
-    flist = phot.load_filters(filters, interp=True, lamb=vl, filterLib=__default_filtlist__)
+    flist = phot.load_filters(
+        filters, interp=True, lamb=vl, filterLib=__default_filtlist__
+    )
 
     fname = []
     cwave = []
@@ -684,21 +686,21 @@ def make_vega_libfile():
         mag.append(-2.5 * np.log10(flux))
 
     contents = np.array(
-            list(
-                zip(
-                    fname,
-                    cwave,
-                    lum,
-                    mag,
-                )
-            ),
-            dtype=[
-                ("FNAME", "S30"),
-                ("CWAVE", "<f8"),
-                ("LUM", "<f8"),
-                ("MAG", "<f8"),
-            ],
-        )
+        list(
+            zip(
+                fname,
+                cwave,
+                lum,
+                mag,
+            )
+        ),
+        dtype=[
+            ("FNAME", "S30"),
+            ("CWAVE", "<f8"),
+            ("LUM", "<f8"),
+            ("MAG", "<f8"),
+        ],
+    )
 
     vega.create_dataset("sed", data=contents)
     vega.close()

From 42a2068a7e09012be57f1b8c85fef3fd8d8e2b48 Mon Sep 17 00:00:00 2001
From: Karl Gordon <kgordon@stsci.edu>
Date: Thu, 15 Feb 2024 16:24:22 -0500
Subject: [PATCH 18/21] making code simpler

---
 beast/tools/make_libfile.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index 28abe18ea..b91e35661 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -678,10 +678,10 @@ def make_vega_libfile():
     lum = []
     mag = []
 
-    for i in range(len(flist)):
-        fname.append(flist[i].name)
-        cwave.append(flist[i].cl)
-        flux = flist[i].getFlux(vl, vf)
+    for cfilt in flist:
+        fname.append(cfilt.name)
+        cwave.append(cfilt.cl)
+        flux = cfilt.getFlux(vl, vf)
         lum.append(flux)
         mag.append(-2.5 * np.log10(flux))
 

From b683663f8e87a822925809f0e431b0dbcc399a17 Mon Sep 17 00:00:00 2001
From: "Karl D. Gordon" <kgordon@stsci.edu>
Date: Sat, 24 Feb 2024 05:41:40 -0500
Subject: [PATCH 19/21] adding filters doc with plots of all filters

---
 beast/plotting/plot_filters.py |  32 ++++----
 beast/tools/make_libfile.py    | 115 +++++------------------------
 docs/beast_setup.rst           | 130 +--------------------------------
 docs/index.rst                 |   1 +
 4 files changed, 39 insertions(+), 239 deletions(-)

diff --git a/beast/plotting/plot_filters.py b/beast/plotting/plot_filters.py
index 1d093d517..05aa135ab 100755
--- a/beast/plotting/plot_filters.py
+++ b/beast/plotting/plot_filters.py
@@ -15,12 +15,10 @@
 def plot_filters(
     filter_names,
     filterLib=None,
-    save_name="beast_filters",
     xlim=None,
     ylim=[1e-4, 2],
     show_plot=True,
 ):
-
     """Plots transmission curves in log-log space.
 
     Parameters
@@ -43,7 +41,7 @@ def plot_filters(
 
     # wavelength grid in angstroms for response functions
     #  cover all HST and JWST wavelengths
-    waves = np.logspace(np.log10(912.), np.log10(3e5), 1001)
+    waves = np.logspace(np.log10(912.0), np.log10(3e5), 1001)
 
     # read in the filter response functions
     flist = phot.load_filters(
@@ -61,24 +59,25 @@ def plot_filters(
     # ax.set_prop_cycle(color=[cmap(i) for i in color_indices])
     color = iter(cmap(np.linspace(0.2, 0.8, len(filter_names))))
 
-    dxlim = [3e5, 912.]
+    dxlim = np.array([3e5, 912.0]) * 1e-4
     for f in flist:
+        wavelength = f.wavelength * 1e-4
         c = next(color)
-        ax.plot(f.wavelength, f.transmit, color=c, lw=2)
-        ax.fill_between(f.wavelength, f.transmit, alpha=0.2, color=c)
+        ax.plot(wavelength, f.transmit, color=c, lw=2)
+        ax.fill_between(wavelength, f.transmit, alpha=0.2, color=c)
         yval_text = max(f.transmit * 0.1)
         ax.text(
-            np.nanmean(f.wavelength[f.transmit > yval_text]),
+            np.nanmean(wavelength[f.transmit > yval_text]),
             1.3 * np.nanmax(f.transmit[f.transmit > yval_text]),
             f.name.split("_")[-1],
             ha="center",
             color=c,
         )
         gvals = (f.transmit > ylim[0]) & (f.transmit < ylim[1])
-        if min(f.wavelength[gvals]) < dxlim[0]:
-            dxlim[0] = min(f.wavelength[gvals])
-        if max(f.wavelength[gvals]) > dxlim[1]:
-            dxlim[1] = max(f.wavelength[gvals])
+        if min(wavelength[gvals]) < dxlim[0]:
+            dxlim[0] = min(wavelength[gvals])
+        if max(wavelength[gvals]) > dxlim[1]:
+            dxlim[1] = max(wavelength[gvals])
 
     if xlim is None:
         xlim = dxlim
@@ -87,11 +86,11 @@ def plot_filters(
     ax.set_yscale("log")
     ax.set_xlim(xlim)
     ax.set_ylim(ylim)
-    ax.set_xlabel(r"$\lambda$ [$\AA$]")
+    ax.set_xlabel(r"$\lambda$ [$\mu m$]")
     ax.set_ylabel(r"$B_i(\lambda)$")
 
     # ax.set_xticks([0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 2.0])
-    ax.get_xaxis().set_major_formatter(mpl.ticker.ScalarFormatter())
+    # ax.get_xaxis().set_major_formatter(mpl.ticker.ScalarFormatter())
 
     fig.tight_layout()
 
@@ -119,10 +118,9 @@ def plot_filters(
         "HST_WFC3_F110W",
         "HST_WFC3_F160W",
     ]
-    parser.add_argument("filter_names",
-                        help="names of filters",
-                        nargs='+',
-                        default=def_filter_names)
+    parser.add_argument(
+        "filter_names", help="names of filters", nargs="+", default=def_filter_names
+    )
     args = parser.parse_args()
 
     fig = plot_filters(args.filter_names, show_plot=False)
diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index b91e35661..a5a4d6752 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -17,104 +17,27 @@ def make_filters_libfile():
     """
     Extract filters from STSYNPHOT and save to main library file.
     """
-    # wfc3_obsmodes_uvis
-    wfc3_uvis = [
-        "f218w",
-        "f225w",
-        "f275w",
-        "f280n",
-        "f336w",
-        "f343n",
-        "f373n",
-        "f390m",
-        "f390w",
-        "f395n",
-        "f410m",
-        "f438w",
-        "f467m",
-        "f469n",
-        "f475w",
-        "f487n",
-        "f502n",
-        "f547m",
-        "f555w",
-        "f606w",
-        "f621m",
-        "f625w",
-        "f631n",
-        "f645n",
-        "f656n",
-        "f657n",
-        "f658n",
-        "f665n",
-        "f673n",
-        "f680n",
-        "f689m",
-        "f763m",
-        "f775w",
-        "f814w",
-        "f845m",
-        "f953n",
-    ]
-
-    wfc3_ir = [
-        "f098m",
-        "f105w",
-        "f110w",
-        "f125w",
-        "f127m",
-        "f139m",
-        "f140w",
-        "f153m",
-        "f160w",
-    ]
-
-    wfpc2 = [
-        "f122m",
-        "f157w",
-        "f336w",
-        "f410m",
-        "f467m",
-        "f547m",
-        "f439w",
-        "f569w",
-        "f675w",
-        "f791w",
-        "f170w",
-        "f185w",
-        "f218w",
-        "f255w",
-        "f300w",
-        "f380w",
-        "f555w",
-        "f622w",
-        "f450w",
-        "f606w",
-        "f702w",
-        "f814w",
-    ]
-
-    acs_wfc = [
-        "f435w",
-        "f475w",
-        "f550m",
-        "f555w",
-        "f606w",
-        "f625w",
-        "f775w",
-        "f814w",
-    ]
-
-    acs_sbc = [
-        "f115lp",
-        "f125lp",
-        "f140lp",
-        "f150lp",
-        "f165lp",
-        "f122m",
-    ]
 
     # fmt: off
+    wfc3_uvis = ["f218w","f225w", "f275w", "f336w", "f390w", "f438w",
+                 "f475w", "f555w", "f606w", "f625w", "f775w", "f814w",
+                 "f390m", "f410m", "f467m", "f547m", "f621m", "f689m", "f763m", "f845m",
+                 "f280n", "f343n", "f373n", "f395n", "f469n", "f487n", "f502n", "f631n",
+                 "f645n", "f656n", "f657n", "f658n", "f665n", "f673n", "f680n", "f953n"]
+
+    wfc3_ir = ["f105w", "f110w", "f125w", "f140w", "f160w",
+               "f098m", "f127m", "f139m", "f153m"]
+
+    wfpc2 = ["f157w", "f170w", "f185w", "f218w", "f255w",
+             "f300w", "f336w", "f380w", "f439w", "f450w", "f555w",
+             "f569w", "f606w", "f622w", "f675w", "f702w", "f791w", "f814w",
+             "f122m", "f410m", "f467m", "f547m"]
+
+    acs_wfc = ["f435w", "f475w", "f555w", "f606w", "f625w", "f775w", "f814w", "f850lp",
+               "f502n", "f550m", "f658n"]
+
+    acs_sbc = ["f115lp", "f125lp", "f140lp", "f150lp", "f165lp", "f122m"]
+
     jwst_nircam_sw = ["f150w2", "f070w", "f090w", "f115w", "f150w", "f200w",
                       "f140m", "f162m", "f182m", "f210m",
                       "f164n", "f187n", "f212n"]
diff --git a/docs/beast_setup.rst b/docs/beast_setup.rst
index d6b4c1f2e..6f43d4293 100644
--- a/docs/beast_setup.rst
+++ b/docs/beast_setup.rst
@@ -137,7 +137,8 @@ BEAST Filters
 =============
 
 The filters are defined in ``beast/libs/filters.hd5``. The file
-has been updated in March, 2022 using stsynphot to have correct, 
+has been updated in Feb 2024 using stsynphot (HST/GALEX) and 
+pandeia (JWST) to have correct, 
 total throughput for HST filters and to remove unused filters. 
 The file contains two groups:
 
@@ -154,128 +155,5 @@ The filters currently included in the BEAST filter library are as follows.
 
 Please do not forget updating ``beast/libs/vega.hd5`` as well when making 
 any updates in ``beast/libs/filters.hd5``. Vega fluxes and magnitudes in 
-udpated filters need to be correspondingly recomputed and saved in vega.hd5.
-
-+--------------------------+
-| HST_WFC3_F218W           |
-+--------------------------+
-| HST_WFC3_F225W           |
-+--------------------------+
-| HST_WFC3_F275W           |
-+--------------------------+
-| HST_WFC3_F336W           |
-+--------------------------+
-| HST_WFC3_F390M           |
-+--------------------------+
-| HST_WFC3_F390W           |
-+--------------------------+
-| HST_WFC3_F410M           |
-+--------------------------+
-| HST_WFC3_F438W           |
-+--------------------------+
-| HST_WFC3_F467M           |
-+--------------------------+
-| HST_WFC3_F475W           |
-+--------------------------+
-| HST_WFC3_F547M           |
-+--------------------------+
-| HST_WFC3_F555W           |
-+--------------------------+
-| HST_WFC3_F606W           |
-+--------------------------+
-| HST_WFC3_F621M           |
-+--------------------------+
-| HST_WFC3_F625W           |
-+--------------------------+
-| HST_WFC3_F689M           |
-+--------------------------+
-| HST_WFC3_F763M           |
-+--------------------------+
-| HST_WFC3_F775W           |
-+--------------------------+
-| HST_WFC3_F814W           |
-+--------------------------+
-| HST_WFC3_F845M           |
-+--------------------------+
-| HST_WFC3_F098M           |
-+--------------------------+
-| HST_WFC3_F105W           |
-+--------------------------+
-| HST_WFC3_F110W           |
-+--------------------------+
-| HST_WFC3_F125W           |
-+--------------------------+
-| HST_WFC3_F127M           |
-+--------------------------+
-| HST_WFC3_F139M           |
-+--------------------------+
-| HST_WFC3_F140W           |
-+--------------------------+
-| HST_WFC3_F153M           |
-+--------------------------+
-| HST_WFC3_F160W           |
-+--------------------------+
-| HST_WFPC2_F122M          |
-+--------------------------+
-| HST_WFPC2_F157W          |
-+--------------------------+
-| HST_WFPC2_F336W          |
-+--------------------------+
-| HST_WFPC2_F410M          |
-+--------------------------+
-| HST_WFPC2_F467M          |
-+--------------------------+
-| HST_WFPC2_F547M          |
-+--------------------------+
-| HST_WFPC2_F439W          |
-+--------------------------+
-| HST_WFPC2_F569W          |
-+--------------------------+
-| HST_WFPC2_F675W          |
-+--------------------------+
-| HST_WFPC2_F791W          |
-+--------------------------+
-| HST_WFPC2_F170W          |
-+--------------------------+
-| HST_WFPC2_F185W          |
-+--------------------------+
-| HST_WFPC2_F218W          |
-+--------------------------+
-| HST_WFPC2_F255W          |
-+--------------------------+
-| HST_WFPC2_F300W          |
-+--------------------------+
-| HST_WFPC2_F380W          |
-+--------------------------+
-| HST_WFPC2_F555W          |
-+--------------------------+
-| HST_WFPC2_F622W          |
-+--------------------------+
-| HST_WFPC2_F450W          |
-+--------------------------+
-| HST_WFPC2_F606W          |
-+--------------------------+
-| HST_WFPC2_F702W          |
-+--------------------------+
-| HST_WFPC2_F814W          |
-+--------------------------+
-| HST_ACS_WFC_F435W        |
-+--------------------------+
-| HST_ACS_WFC_F475W        |
-+--------------------------+
-| HST_ACS_WFC_F550M        |
-+--------------------------+
-| HST_ACS_WFC_F555W        |
-+--------------------------+
-| HST_ACS_WFC_F606W        |
-+--------------------------+
-| HST_ACS_WFC_F625W        |
-+--------------------------+
-| HST_ACS_WFC_F775W        |
-+--------------------------+
-| HST_ACS_WFC_F814W        |
-+--------------------------+
-| GALEX_FUV                |
-+--------------------------+
-| GALEX_NUV                |
-+--------------------------+
+updated filters need to be correspondingly recomputed and saved in vega.hd5.
+See :doc:`beast_filters` for the full current set of included filters.
diff --git a/docs/index.rst b/docs/index.rst
index 920022309..57fd9a863 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -30,6 +30,7 @@ Basics:
    :maxdepth: 1
 
    Run setup <beast_setup.rst>
+   Filters supported <beast_filters.rst>
    Photometry files <photometry_files.rst>
    Output files <outputs.rst>
 

From d2a0790aaacd72a002518cf362c9a0a2e3364e91 Mon Sep 17 00:00:00 2001
From: "Karl D. Gordon" <kgordon@stsci.edu>
Date: Sat, 24 Feb 2024 05:50:15 -0500
Subject: [PATCH 20/21] adding in missing doc file

---
 beast/tools/make_libfile.py |   2 +-
 docs/beast_filters.rst      | 257 ++++++++++++++++++++++++++++++++++++
 2 files changed, 258 insertions(+), 1 deletion(-)
 create mode 100644 docs/beast_filters.rst

diff --git a/beast/tools/make_libfile.py b/beast/tools/make_libfile.py
index a5a4d6752..742369774 100644
--- a/beast/tools/make_libfile.py
+++ b/beast/tools/make_libfile.py
@@ -19,7 +19,7 @@ def make_filters_libfile():
     """
 
     # fmt: off
-    wfc3_uvis = ["f218w","f225w", "f275w", "f336w", "f390w", "f438w",
+    wfc3_uvis = ["f218w", "f225w", "f275w", "f336w", "f390w", "f438w",
                  "f475w", "f555w", "f606w", "f625w", "f775w", "f814w",
                  "f390m", "f410m", "f467m", "f547m", "f621m", "f689m", "f763m", "f845m",
                  "f280n", "f343n", "f373n", "f395n", "f469n", "f487n", "f502n", "f631n",
diff --git a/docs/beast_filters.rst b/docs/beast_filters.rst
new file mode 100644
index 000000000..ecbd3da6f
--- /dev/null
+++ b/docs/beast_filters.rst
@@ -0,0 +1,257 @@
+#######
+Filters
+#######
+
+Filters included in the BEAST
+
+Hubble
+======
+
+WFC3
+----
+
+Imaging, UVIS, Wide
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   wfc3_uvis = ["f218w","f225w", "f275w", "f336w", "f390w", "f438w",
+                "f475w", "f555w", "f606w", "f625w", "f775w", "f814w"]
+   filters = [f"HST_WFC3_{cfilt.upper()}" for cfilt in wfc3_uvis]
+   plot_filters(filters)
+
+Imaging, UVIS, Medium
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   wfc3_uvis = ["f390m", "f410m", "f467m", "f547m", "f621m", "f689m", "f763m", "f845m"]
+   filters = [f"HST_WFC3_{cfilt.upper()}" for cfilt in wfc3_uvis]
+   plot_filters(filters)
+
+Imaging, UVIS, Narrow, Blue
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   wfc3_uvis = ["f280n", "f343n", "f373n", "f395n", "f469n", "f487n", "f502n", "f631n"]
+   filters = [f"HST_WFC3_{cfilt.upper()}" for cfilt in wfc3_uvis]
+   plot_filters(filters)
+
+Imaging, UVIS, Narrow, Red 
+(Note: F656N not included, error when plotting)
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   wfc3_uvis = ["f645n", "f657n", "f658n", "f665n", "f673n", "f680n", "f953n"]
+   filters = [f"HST_WFC3_{cfilt.upper()}" for cfilt in wfc3_uvis]
+   plot_filters(filters)
+
+Imaging, IR, wide
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   wfc3_ir = ["f105w", "f110w", "f125w", "f140w", "f160w"]
+   filters = [f"HST_WFC3_{cfilt.upper()}" for cfilt in wfc3_ir]
+   plot_filters(filters)
+
+Imaging, IR, medium
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   wfc3_ir = ["f098m", "f127m", "f139m", "f153m"]
+   filters = [f"HST_WFC3_{cfilt.upper()}" for cfilt in wfc3_ir]
+   plot_filters(filters)
+
+ACS
+---
+
+Imaging, WFC, wide
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   acs_wfc = ["f435w", "f475w", "f555w", "f606w", "f625w", "f775w", "f814w"]
+   filters = [f"HST_ACS_WFC_{cfilt.upper()}" for cfilt in acs_wfc]
+   plot_filters(filters)
+
+
+Imaging, WFC, extrawide, medium and narrow
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   acs_wfc = ["f850lp", "f502n", "f550m", "f658n"]
+   filters = [f"HST_ACS_WFC_{cfilt.upper()}" for cfilt in acs_wfc]
+   plot_filters(filters)
+
+Imaging, SBC
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   acs_sbc = ["f115lp", "f125lp", "f140lp", "f150lp", "f165lp", "f122m"]
+   filters = [f"HST_ACS_SBC_{cfilt.upper()}" for cfilt in acs_sbc]
+   plot_filters(filters)
+
+WFPC2
+-----
+
+Imaging, UV, Wide
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   wfpc2 = ["f157w", "f170w", "f185w", "f218w", "f255w", "f300w"]
+   filters = [f"HST_WFPC2_{cfilt.upper()}" for cfilt in wfpc2]
+   plot_filters(filters)
+
+Imaging, Optical, Blue
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   wfpc2 = ["f336w", "f380w", "f439w", "f450w", "f555w", "f569w"]
+   filters = [f"HST_WFPC2_{cfilt.upper()}" for cfilt in wfpc2]
+   plot_filters(filters)
+
+Imaging, Optical, Red
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   wfpc2 = ["f606w", "f622w", "f675w", "f702w", "f791w", "f814w"]
+   filters = [f"HST_WFPC2_{cfilt.upper()}" for cfilt in wfpc2]
+   plot_filters(filters)
+
+Imaging, Medium
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   wfpc2 = ["f122m", "f410m", "f467m", "f547m"]
+   filters = [f"HST_WFPC2_{cfilt.upper()}" for cfilt in wfpc2]
+   plot_filters(filters)
+
+Webb
+====
+
+NIRCam
+------
+
+Imaging, Very Wide Bands
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   jwst_nircam = ["f150w2", "f332w2"]
+   filters = [f"JWST_NIRCAM_{cfilt.upper()}" for cfilt in jwst_nircam]
+   plot_filters(filters)
+
+Imaging, Wide Bands
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   jwst_nircam = ["f070w", "f090w", "f115w", "f150w", "f200w",
+                  "f277w", "f356w", "f444w"]
+   filters = [f"JWST_NIRCAM_{cfilt.upper()}" for cfilt in jwst_nircam]
+   plot_filters(filters)
+
+Imaging, Medium Bands
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   jwst_nircam = ["f140m", "f162m", "f182m", "f210m",
+                  "f250m", "f300m", "f335m", "f360m", "f410m", "f430m", "f460m", "f480m"]
+   filters = [f"JWST_NIRCAM_{cfilt.upper()}" for cfilt in jwst_nircam]
+   plot_filters(filters)
+
+Imaging, Narrow Bands
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   jwst_nircam = ["f164n", "f187n", "f212n",
+                  "f323n", "f405n", "f466n", "f470n"]
+   filters = [f"JWST_NIRCAM_{cfilt.upper()}" for cfilt in jwst_nircam]
+   plot_filters(filters)
+
+NIRISS
+------
+
+Imaging, Wide Bands
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   jwst_niriss = ["f090w", "f115w", "f150w", "f200w", "f277w", "f356w", "f444w"]
+   filters = [f"JWST_NIRISS_{cfilt.upper()}" for cfilt in jwst_niriss]
+   plot_filters(filters)
+
+Imaging, Medium Bands
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   jwst_niriss = ["f140m", "f158m", "f380m", "f430m", "f480m"]
+   filters = [f"JWST_NIRISS_{cfilt.upper()}" for cfilt in jwst_niriss]
+   plot_filters(filters)
+
+MIRI
+----
+
+Imaging
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   jwst_miri = ["f560w", "f770w", "f1000w", "f1130w", "f1280w", "f1500w", "f1800w", "f2100w", "f2550w"]
+   filters = [f"JWST_MIRI_{cfilt.upper()}" for cfilt in jwst_miri]
+   plot_filters(filters)
+
+Coronagraphy
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   jwst_miri = ["f1065c", "f1140c", "f1550c", "f2300c"]
+   filters = [f"JWST_MIRI_{cfilt.upper()}" for cfilt in jwst_miri]
+   plot_filters(filters)
+
+GALEX
+=====
+
+Imaging
+
+.. plot::
+
+   from beast.plotting.plot_filters import plot_filters
+
+   plot_filters(["GALEX_FUV", "GALEX_NUV"])
+

From 55b1560901071c45689bf8c11975d370bb181efe Mon Sep 17 00:00:00 2001
From: "Karl D. Gordon" <kgordon@stsci.edu>
Date: Sat, 24 Feb 2024 05:59:27 -0500
Subject: [PATCH 21/21] adding in filters download for RTD build

---
 docs/beast_filters.rst | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/docs/beast_filters.rst b/docs/beast_filters.rst
index ecbd3da6f..e9364b1f1 100644
--- a/docs/beast_filters.rst
+++ b/docs/beast_filters.rst
@@ -16,6 +16,10 @@ Imaging, UVIS, Wide
 
    from beast.plotting.plot_filters import plot_filters
 
+   # required to get the filters library needed for building on RTD
+   from beast.tools import get_libfiles
+   get_libfiles.get_libfiles(vega_filters_only=True)
+
    wfc3_uvis = ["f218w","f225w", "f275w", "f336w", "f390w", "f438w",
                 "f475w", "f555w", "f606w", "f625w", "f775w", "f814w"]
    filters = [f"HST_WFC3_{cfilt.upper()}" for cfilt in wfc3_uvis]