SpectraFit can be currently only installed directly from the GitHub
repository. It is important that poetry is installed first, because the
setup.py is not explicitly defined, because it is indirectly available in the
pyproject.toml file.
pip install git+https://github.com/Anselmoo/SpectraFit.gitpip install spectrafitFor the jupyter support, the following command can be used:
pip install spectrafit[jupyter-dash]For the graph visualization, the following command can be used:
pip install spectrafit[graph]For all extensions, the following command can be used:
pip install spectrafit[all]To keep the system environment clean, the installation is done via the:
=== "PIPX"
[PIPX][1] allows to install and run packages in a _isolated_ environment.
_Installation_:
```bash
# install pipx for macOS
brew install pipx
# install pipx for Linux or Windows
pip install pipx
pipx install --upgrade pipx
# install spectrafit for python 3.7
pipx install spectrafit --python python3.7
# install spectrafit for python 3.8
pipx install spectrafit --python python3.8
# install spectrafit for python 3.9
pipx install spectrafit --python python3.9
spectrafit --help
```
=== "Conda"
[Conda][2] is a package manager for Python. It is a tool for installing and
managing packages, environments, and virtualenvs. `SpectraFit` is available as [conda-forge][3].
_Example_:
```bash
conda install -c conda-forge spectrafit
spectrafit --help
```
For include the `jupyter` support, the following command can be used:
```bash
conda install -c conda-forge spectrafit-jupyter
# To test
python -c "from spectrafit.plugins.notebook import SpectraFitNotebook"
```
For include the `graph` support, the following command can be used:
```bash
conda install -c conda-forge spectrafit-graph
# To test
python -c "from spectrafit.plugins.graph import SpectraFitGraph"
```
For include the `all` support, the following command can be used:
```bash
conda install -c conda-forge spectrafit-all
# To test
python -c "from spectrafit.plugins.notebook import SpectraFitNotebook"
python -c "from spectrafit.plugins.graph import SpectraFitGraph"
```
Extended documentation about the installation of `SpectraFit` via conda can
be found [here][7]. In general, the following command can be useful for
working with conda:
```bash
conda config --add channels conda-forge
conda config --set channel_priority strict
```
=== "Poetry"
For installing `SpectraFit` via [Poetry][8], first `SpectraFit` has to be
downloaded or cloned from the [GitHub repository][9]. Optionally, the
`SpectraFit` repo has to be unpacked. Next, `poetry` has to be installed
via `pip`:
```bash
pip install poetry
```
or via `conda`:
```bash
conda install -c conda-forge poetry
```
_Installation_:
```bash
poetry install -E jupyter
```
_Usage_:
```bash
poetry run spectrafit --help
```
or using the `poetry shell`:
```bash
poetry shell
spectrafit --help
```
Result:
usage: spectrafit [-h] [-o OUTFILE] [-i INPUT] [-ov] [-e0 ENERGY_START]
[-e1 ENERGY_STOP] [-s SMOOTH] [-sh SHIFT] [-c COLUMN COLUMN]
[-sep { ,,,;,:,|, ,s+}] [-dec {.,,}] [-hd HEADER]
[-g {0,1,2}] [-auto] [-np] [-v] [-vb {0,1,2}]
infile
Fast Fitting Program for ascii txt files.
...The SpectraFit package is designed to be extended by plugins. Currently
available plugins are:
- Input-File-Converter (built-in)
- Jupyter-Notebook-Interface (
pip install spectrafit[jupyter]) - Elastic-Line-Alignment (in progress)
!!! info "About Docker-Image"
Since version 0.12.0, the `SpectraFit` package is available as a
[Docker-Image][4]. The Docker-Image is based on an modified
[Jupyter-Scipy-Image][5] and contains the `SpectraFit` package and
the [Jupyter-Notebook][6] interface.
> The Docker-Image can be installed for both **amd64** aka **x86_64** or
> **arm64** and used via:
```bash
docker pull ghcr.io/anselmoo/spectrafit:latest
docker run -it -p 8888:8888 spectrafit:latest
```
or just via:
```bash
docker run -it -p 8888:8888 ghcr.io/anselmoo/spectrafit:latest
```
To include the _home directory_ of the host system, the following command can
be used:
```bash
docker run -it -p 8888:8888 -v $HOME:/home/user/work spectrafit:latest
```
or via:
```bash
docker run -it -p 8888:8888 -v $HOME:/home/user/work ghcr.io/anselmoo/spectrafit:latest
```
see also: [spectrafit](https://github.com/Anselmoo/spectrafit/pkgs/container/spectrafit)
!!! info "About cosign"
The `cosign` is a tool for signing and verifying container images as part of the
[sigstore][10] project.The `cosign` can be used to sign the `SpectraFit` container
image. The `cosign` can be [installed][11] via:
```bash
# install cosign for macOS and Linux
brew install cosign
# install cosign via go
go install github.com/sigstore/cosign/v2/cmd/cosign@latest
```
To verify the SpectraFit container image, SpectraFit's public key is required and
can be found under: https://github.com/Anselmoo/spectrafit/blob/main/cosign.pub.
You can save the public key to a file named cosign.pub:
```bash
cat cosign.pub
-----BEGIN PUBLIC KEY-----
MFkwEwYHKoZIzj0CAQYIKoZIzj0DAQcDQgAE/6fPQhwVsFvcfGtSFBIwdHbTxkF3
KaNOdpXBpmyrM/y1TM5YgTYl5mVq7km/LPukbXslcrVX1dT5H+FUP6+onQ==
-----END PUBLIC KEY-----
```
Then, cosign can be used to verify the SpectraFit container image:
```bash
cosign verify --key cosign.pub ghcr.io/anselmoo/spectrafit:latest
# or export to json
cosign verify --key cosign.pub ghcr.io/anselmoo/spectrafit:latest > cosign_verify.json
```
and the output can be saved to a file named `cosign_verify.json`.
```bash
cat cosign_verify.json
[
{
"critical": {
"identity": {
"docker-reference": "ghcr.io/anselmoo/spectrafit"
},
...
```