Installation¶

Installing Chem-I-Calc¶

Chem-I-Calc is written in pure Python and can be easily installed from GitHub (and soon also through PyPI). It requires Python 3.6 or later. We recommend that users install Chem-I-Calc and its Python dependencies in a dedicated Conda environment (or other virtual Python environment).

From GitHub¶

The source code for Chem-I-Calc can be downloaded from GitHub and installed by running

cd <path_to_installation>
git clone https://github.com/nathansandford/Chem-I-Calc.git
cd Chem-I-Calc
python setup.py develop

Testing

You can test your installation by running pytest in the installation directory.

pip install pytest  # if pytest not already installed
pytest -v

Note however, that the unit tests are still under active development. Many tests are presently skipped and several are expected to fail.

Downloading Data¶

Chem-I-Calc requires grids of high-resolution spectra to calculate partial derivatives of a star’s spectrum for a wide variety of instrumental configurations. Unfortunately, the file containing our pre-generated grids of spectra, reference_spectra_300000.h5, is too large to host on Github or PyPi (~11 Gb) and must be downloaded seperately. You have three options to acquire this file.

At Runtime¶

If you run any portion of the code that requires reference_spectra_300000.h5 and the file cannot be found in PATH_TO_INSTALLATION/Chem-I-Calc/chemicalc/data/, the file will automatically be downloaded to the appropriate directory in chunks of 32768 bytes. For example, the following code will initiate the download.

import chemicalc.reference_spectra as ref

RGB = ref.ReferenceSpectra(reference="RGB_m1.5")

With `chemicalc.file_mgmt.download_all_files()`¶

You can also manually call the python function that begins the download process. This can also be used to re-download reference_spectra_300000.h5 in the case that it has been updated. This will also re-download reference_labels.h5, though it should already be kept up to date through standard version control methods (i.e., via GitHub and PyPi).

from chemicalc.file_mgmt import download_all_files

download_all_files(overwrite=True)

Manually¶

The file is hosted on Google Drive, so it is also possible to manually download reference_spectra_300000.h5 using the following link:

You will need to place this file in the appropriate directory:

PATH_TO_INSTALLATION/Chem-I-Calc/chemicalc/data/

If you are unsure what the full path to the directory is, you can check with the following code:

from chemicalc.file_mgmt import data_dir

print(data_dir)

Python Dependencies¶

Chem-I-Calc depends on the following list of Python packages. They should be installed automatically with Chem-I-Calc when following either installation method below. Additional optional dependencies can be found below.

python version 3.6 or later
numpy version 1.18.0 or later
pandas version 1.0.0 or later
scipy version 1.4.0 or later
tables version 3.6.0 or later
mendeleev version 0.6.0 or later
mechanicalsoup version 0.12.0 or later
requests version 2.23.0 or later
matplotlib version 3.2.0 or later
setuptools version 45.2.0 or later
pytest version 5.0.0 or later

Note

The version requirements for these packages can likely be relaxed, but we have yet to determine which ones and to what extent.

Optional Dependencies¶

The following packages are not required to use most of Chem-I-Calc’s functionality. Feel free to install some or all of them as they are applicable to your work.

Working in Notebooks¶

To use Chem-I-Calc in an interactive Python notebook, you will need to install:

ipython
jupyter or jupyterlab

ETC Querying¶

While some spectrographs have online exposure time calculators (ETCs) that can be queeried by Chem-I-Calc, others have ETCs in the form of GitHub code repositories. To simplify the installation of Chem-I-Calc, we do not include these repositories as dependencies. However, to ease the integration of those ETC’s with Chem-I-Calc, we have written several convenience functions into chemicalc.s2n. To use these functions, you will need to install the relevant repositories following the instructions below.

Warning

Many of these repositories are undergoing constant revision so we recommend making sure that you have the most recent version installed before making important calculations. If a ETC code-base changes sufficiently that it breaks the Chem-I-Calc interface with them, please raise an issue on the Chem-I-Calc GitHub.

Note

If you know of any additional ETC codes that you would like to integrate with Chem-I-Calc, please don’t hesitate to reach out. We would love to include them!

FOBOS ETC (enyo)¶

To use chemicalc.s2n.calculate_fobos_snr() the fobos-enyo package must be installed as follows:

cd PATH_TO_INSTALLATION
git clone https://github.com/Keck-FOBOS/enyo
cd enyo
python setup.py develop

To update:

cd PATH_TO_INSTALLATION/enyo
git pull
python setup.py develop

PFS ETC¶

No convenience functions have been writted for the PFS ETC, but it was used for Sandford et al. (in prep). To install:

cd PATH_TO_INSTALLATION
git clone https://github.com/Subaru-PFS/spt_ExposureTimeCalculator
cd enyo
python setup.py develop