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Merge pull request #160 from spacetelescope/dev
merge changes to Readme, local files and pandeia notebook
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‎README.md‎

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@@ -10,33 +10,12 @@ Notebook tutorials are organized under the `content/notebooks/` directory. Each
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Markdown documentation files are contained within the `markdown/` folder.
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## Local Installation (Not Recommended)
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## Local Installation
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The notebooks in this repository are designed to work on the Roman Research Nexus for the best user experience. Due to the size of Roman data, local use is not recommended for most users. However, we provide instructions for local installation below.
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The notebooks contained in this repository can be run locally with the correct environment setup. It is recommended to create a new environment (e.g., with [mamba](https://mamba.readthedocs.io/en/latest/index.html)) to run the tutorials. For example:
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```
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mamba create -n roman-notebooks python ipython jupyterlab
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```
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Each notebook folder includes a `requirements.txt` file with the necessary Python package versions listed. To install package dependencies from a `requirements.txt` file with `pip`, first navigate to a notebook folder and then use the following command:
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```
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pip install -r requirements.txt
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```
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Several notebooks use packages that require supplementary data to be installed (e.g., `stpsf` for generating Roman Wide Field Instrument point spread functions). In those instances, a Python script is called at the beginning of the notebook to check for these data dependencies, download the appropriate data files if they are not found, and instruct you on how to set the correct environment variables.
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Additionally, a correctly configured [Calibration Reference Data System](https://roman-crds.stsci.edu/static/users_guide/index.html) setup is required to simulate and/or calibrate Roman observations. Please set the environment variable below:
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```
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export CRDS_SERVER_URL = "https://roman-crds.stsci.edu"
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export CRDS_PATH = "/path/to/crds/cache/"
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```
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where `CRDS_PATH` points to your CRDS cache. If you do not have a cache already, the directory will be created the first time CRDS is used in the notebooks, but the path must still be set in advance.
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Note that any embedded, relative links to markdown files and other notebook tutorials may not work if the repository is cloned and modified or if files are selectively installed.
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The notebooks in this repository are designed to work on the Roman Research Nexus for the best user experience. Due to the size of Roman data, local use is not recommended for most users. However, we provide instructions for local installation below. For detailed instructions refer to the [**Working Localy**](markdown/local-run.md) instructions.
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## Get Support
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Please refer to the [Roman Documentation (RDox)](https://roman-docs.stsci.edu) website for technical documentation about the Roman Space Telescope.
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If you need assistance, please submit a ticket through the [Roman Help Desk](https://romanhelp.stsci.edu) portal. Once logged into the help desk, click on "Get Help with the Roman Space Telescope" and then select the "Roman Research Nexus" category and submit your ticket.
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If you need assistance, please submit a ticket through the [Roman Help Desk](https://romanhelp.stsci.edu) portal. Once logged into the help desk, click on "Get Help with the Roman Space Telescope" and then select the "Roman Research Nexus" category and submit your ticket.

‎markdown/local-run.md‎

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## Setting up the environment for all notebooks
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Not every notebook in this repository uses the same dependencies. For reproducibility and to avoid conflicts, each notebook folder contains its own requirements.txt file listing only the packages required for that specific notebook.
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The notebooks were tested with Python 3.13, earlier and later versions might not have the desired results. Also note, not every notebook in this repository uses the same dependencies. For reproducibility and to avoid conflicts, each notebook folder contains its own requirements.txt file listing only the packages required for that specific notebook.
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The recommended steps:
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Additionally, a correctly configured [Calibration Reference Data System](https://roman-crds.stsci.edu/static/users_guide/index.html) setup is required to simulate and/or calibrate Roman observations. Please set the environment variable below:
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```
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export CRDS_SERVER_URL = "https://roman-crds.stsci.edu"
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export CRDS_PATH = "/path/to/crds/cache/"
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export CRDS_SERVER_URL="https://roman-crds.stsci.edu"
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export CRDS_PATH="/path/to/crds/cache/"
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```
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where `CRDS_PATH` points to your CRDS cache. If you do not have a cache already, the directory will be created the first time CRDS is used in the notebooks, but the path must still be set in advance.
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In the commnad line or permanently in your shell profile (e.g., ~/.bashrc, ~/.zshrc):
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export STSPSF_PATH="/your/preferred/path/to/stpsf_data"
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```
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export STSPSF_PATH="/your/preferred/path/to/stpsf_data"
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```
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You can also add a cell in your notebook with the following code:
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```os.environ['STSPSF_PATH'] = "/your/preferred/path/to/stpsf_data"```
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```
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os.environ['STSPSF_PATH'] = "/your/preferred/path/to/stpsf_data"
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```
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this cell should be run before the first code cell in the notebook. This is in particular useful with you re-run your notebook and you did not set this environment variable in your shell profile.
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If you wish to re-download the data files, even after setting the environment variable, you can accomplish this in the command line with:
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unset STSPSF_PATH
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```
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unset STSPSF_PATH
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```
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for the `STSPSF_PATH` environment variable. Or in the notebook:
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```os.environ.pop('STSPSF_PATH', None)```
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```
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os.environ.pop('STSPSF_PATH', None)
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```
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Depending on which (if any) reference data are missing, this cell may take several minutes to execute.

‎notebooks/pandeia/pandeia.ipynb‎

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"\n",
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"This notebook walks through brief examples of common use cases.\n",
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"\n",
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"The cell below will check to ensure ancillary reference files for `pandeia` package are installed. If not, it will download the ancillary reference files and install them under your home directory (i.e., `${HOME}/refdata/`).\n",
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"\n",
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"### Local Run Settings\n",
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"\n",
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"If you want to run the notebook in your local machine, refer to the information in [local installation](../../markdown/local-run.md) instructions before proceeding with the notebook. The instructions provide inportant information about setting up your environment, installing dependnecies, and adding to your working directory scripts to help with the reference data installation.\n",
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"\n",
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"Depending on which (if any) reference data are missing, this cell may take several minutes to execute.\n",
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"\n",
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"### On the Roman Research Nexus\n",
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"\n",
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"If you are working on the Nexus, then the ancillary reference data are pre-installed and this cell will execute instantly."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "2e7fbfae",
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"metadata": {},
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"outputs": [],
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"source": [
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"import os\n",
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"import sys\n",
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"import importlib.util\n",
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"\n",
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"try:\n",
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" import notebook_data_dependencies as ndd\n",
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" local = True\n",
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"except ImportError:\n",
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" local = False\n",
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"\n",
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"# If running locally Get the directory with the script\n",
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"if not local:\n",
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" notebook_dir = os.getcwd()\n",
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" shared_path = os.path.abspath(\n",
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" os.path.join(notebook_dir, '..', '..', 'shared', 'notebook_data_dependencies.py')\n",
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" )\n",
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"\n",
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" if os.path.exists(shared_path):\n",
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" print(f\"Loading notebook_data_dependencies from shared location: {shared_path}\")\n",
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" spec = importlib.util.spec_from_file_location(\"notebook_data_dependencies\", shared_path)\n",
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" ndd = importlib.util.module_from_spec(spec)\n",
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" sys.modules['notebook_data_dependencies'] = ndd # Optional: makes subsequent imports work\n",
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" spec.loader.exec_module(ndd)\n",
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" else:\n",
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" raise FileNotFoundError(f\"Local install script not found at {shared_path}\")\n",
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"\n",
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"if not local:\n",
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" print(\"Running local data dependency installation...\")\n",
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" result = ndd.install_files(packages=['pandeia'])\n",
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"\n",
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" # Update environment variables (if necessary) and print reference data paths\n",
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" print('Reference data paths set to:')\n",
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" for k, v in result.items():\n",
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" if not v['pre_installed']:\n",
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" os.environ[k] = v['path']\n",
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" print(f\"\\t{k} = {v['path']}\")\n",
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"\n",
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"else:\n",
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" print(\"Running on RNN — data already available, skipping local install.\")\n"
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]
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},
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{
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"cell_type": "markdown",
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"id": "b8e2590e",
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"metadata": {},
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"source": [
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"## Imports\n",
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"\n",
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"Besides the Pandeia-related imports, we will use `scipy.optimize.minimize_scalar` to help with optimizing signal-to-noise ratios (SNRs), `scipy.interpolate.interp1d` to calculate a desired target magnitude for a given observing setup and `numpy` to handle numerical computing."

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