Merge pull request #14 from rs-station/main

fast-forward "updates" branch

_data/navbar.yml

@@ -6,5 +6,5 @@
   link: /contact.html
 - name: Publications
   link: /publications.html
-- name: Blog
-  link: /blog.html
+- name: Installation
+  link: /installation.html

_data/packages.yml

@@ -5,8 +5,20 @@
 - name: careless
   link: https://github.com/rs-station/careless
   desc: Applying variational inference to the scaling and merging of crystallographic data
+- name: matchmaps
+  link: https://github.com/rs-station/matchmaps
+  docs: https://rs-station.github.io/matchmaps/
+  desc: Make difference maps between near-isomorphous or non-isomorphous datasets
+- name: laue-dials
+  link: https://github.com/rs-station/laue-dials
+  docs: https://rs-station.github.io/laue-dials/
+  desc: Extending `DIALS` for polychromatic "pink beam" data collected at Laue X-ray sources
+#- name: abismal
+#  link: https://github.com/rs-station/abismal
+#  desc: "**A**pproximate **B**ayesian **I**nference for **S**caling and **M**erging at **A**dvanced **L**ightsources"
 - name: rs-booster
   link: https://github.com/rs-station/rs-booster
+  docs: https://rs-station.github.io/rs-booster/
   desc: A "booster rocket" for `reciprocalspaceship` containing useful command-line utilities
 - name: careless examples
   link: https://github.com/rs-station/careless-examples

_data/publications.yml

@@ -1,15 +1,48 @@
+- nickname: jackdhfr
+  title: "Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism"
+  first_author: "Greisman"
+  authors: "**, Jack B.** Kevin M. Dalton, Dennis E. Brookner, Margaret A. Klureza, Candice J. Sheehan, In-Sik Kim, Robert W. Henning, Silvia Russi, Doeke R. Hekstra"
+  url: https://www.pnas.org/doi/abs/10.1073/pnas.2313192121
+  info: PNAS, 2024
+- nickname: matchmaps
+  title: "MatchMaps: non-isomorphous difference maps for X-ray crystallography"
+  first_author: "Brookner"
+  authors: "**, Dennis E.** and Doeke R, Hekstra"
+  url: https://journals.iucr.org/j/issues/2024/03/00/ei5112/index.html
+  info: Journal of Applied Crystallography, 2024
+- nickname: trxreview
+  title: "Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics"
+  first_author: "Hekstra"
+  authors: "**, Doeke R.**"
+  url: https://www.annualreviews.org/content/journals/10.1146/annurev-biophys-111622-091155
+  info: Annu. Rev. Biophys., 2023
+- nickname: scaling
+  title: "Correcting systematic errors in diffraction data with modern scaling algorithms"
+  first_author: "Aldama"
+  authors: "**, Luis A** and Kevin M. Dalton, Doeke R. Hekstra"
+  url: https://journals.iucr.org/d/issues/2023/09/00/qi5002/index.html
+  info: Acta Crystallographica D, 2023
+- nickname: neurips2022
+  title: "Online Inference of Structure Factor Amplitudes for Serial X-ray Crystallography"
+  first_author: "Dalton"
+  authors: "**, Kevin M.** and Doeke R. Hekstra"
+  url: https://www.mlsb.io/papers_2022/Online_Inference_of_Structure_Factor_Amplitudes_for_Serial_X_ray_Crystallography.pdf
+  info: Machine Learning for Structural Biology Workshop, NeurIPS 2022
 - nickname: careless
   title: "A unifying Bayesian framework for merging X-ray diffraction data"
-  authors: "**Dalton, KM** and Jack B. Greisman, Doeke R. Hekstra"
+  first_author: "Dalton"
+  authors: "**, Kevin M.** and Jack B. Greisman, Doeke R. Hekstra"
   url: https://www.nature.com/articles/s41467-022-35280-8
   info: Nature Communications, 2022
 - nickname: rtsad
   title: Native SAD phasing at room temperature
-  authors: "**Greisman, JB** and Kevin M. Dalton, Candice J. Sheehan, Margaret A. Klureza, Igor Kurinov, Doeke R. Hekstra"
+  first_author: "Greisman"
+  authors: "**, Jack B.** and Kevin M. Dalton, Candice J. Sheehan, Margaret A. Klureza, Igor Kurinov, Doeke R. Hekstra"
   url: https://doi.org/10.1107/S2059798322006799
   info: Acta Crystallographica D, 2022
 - nickname: rs
   title: "*reciprocalspaceship*: a Python library for crystallographic data analysis"
-  authors: "**Greisman, JB** and Kevin M. Dalton, Doeke R. Hekstra"
+  first_author: "Greisman"
+  authors: "**, Jack B.** and Kevin M. Dalton, Doeke R. Hekstra"
   url: https://scripts.iucr.org/cgi-bin/paper?S160057672100755X
   info: Journal of Applied Crystallography, 2021

assets/css/styles.css

@@ -310,6 +310,8 @@ pre code {
   font-size: inherit;
   color: inherit;
   word-break: normal;
+  display: block;
+  margin-left: 12px;
 }
 
 code {

installation.md

@@ -0,0 +1,40 @@
+---
+title: Installation
+layout: content_page
+---
+
+# How to install
+
+All of the Reciprocal Space Station packages are `pip`-installable, e.g.:
+
+```bash
+pip install reciprocalspaceship
+```
+
+We recommend that you use a package manager such as [`conda`](https://docs.conda.io/en/latest/) and always install into a fresh environment, e.g.:
+
+```bash
+conda create -n my-new-careless-environment
+conda activate my-new-careless-environment
+pip install careless
+```
+
+## Development builds
+
+If you're looking for a version of the software that's newer than the latest version published to PyPI, you can alternatively install directly from source:
+
+```bash
+pip install git+https://github.com/rs-station/rs-booster.git
+```
+
+or if you want to develop yourself and use your own custom version, you can clone the source code:
+
+```bash
+git clone https://github.com/rs-station/rs-booster.git
+cd rs-booster
+pip install -e .
+```
+
+## Companion software
+
+The pure-python dependencies of RSS packages (`numpy`, `pandas`, `gemmi`, etc.) will be downloaded automatically when you use `pip`. However, some functionality (e.g. [`rs.scaleit`](https://rs-station.github.io/rs-booster/misc.html#id1) from `rs-booster`) is just a wrapper around other software (in this case, [`CCP4`](https://www.ccp4.ac.uk/download/#os=mac)) which does need to be installed separately. Hopefully, some day soon, software such as `CCP4` and `phenix` will follow the lead of `dials`, `gemmi`, `cctbx`, and more and become `pip`/`conda`-installable!

publications.md

@@ -7,23 +7,37 @@ layout: content_page
 The following publications make use of RSS packages. If there's a paper we're missing, or you've recently published a paper using an RSS package, please [let us know!](/contact.html)
 
 {% for pub in site.data.publications %}
- - [{{ pub.title }}]({{ pub.url}}). {{ pub.authors }}. *{{ pub.info }}*
+ - [{{ pub.title }}]({{ pub.url}}), {{ pub.first_author }} et. al. *{{ pub.info }}*
 {% endfor %}
+
 ---
+
 ## How to cite
 If you're making use of any RSS packages, amazing! Please cite them as follows:
 
-### ReciprocalSpaceship
+### reciprocalspaceship
 {% assign rspub = site.data.publications | where: "nickname", "rs" %}
 {% for pub in rspub %}
-[{{ pub.title }}]({{ pub.url}}). {{ pub.authors }}. *{{ pub.info }}*
+[{{ pub.title }}]({{ pub.url}}). **{{ pub.first_author }}**{{ pub.authors }}. *{{ pub.info }}*
 {% endfor %}
 
-### Careless
+### careless
 {% assign clpub = site.data.publications | where: "nickname", "careless" %}
 {% for pub in clpub %}
-[{{ pub.title }}]({{ pub.url}}). {{ pub.authors }}. *{{ pub.info }}*
+[{{ pub.title }}]({{ pub.url}}). **{{ pub.first_author }}**{{ pub.authors }}. *{{ pub.info }}*
+{% endfor %}
+
+### matchmaps
+{% assign mmpub = site.data.publications | where: "nickname", "matchmaps" %}
+{% for pub in mmpub %}
+[{{ pub.title }}]({{ pub.url}}). **{{ pub.first_author }}**{{ pub.authors }}. *{{ pub.info }}*
 {% endfor %}
 
-### RS-booster
-[Cite GitHub directly](https://github.com/rs-station/rs-booster)
+### laue-dials
+[Cite GitHub directly](https://github.com/rs-station/laue-dials)
+
+### abismal
+[Cite GitHub directly](https://github.com/rs-station/abismal)
+
+### rs-booster
+[Cite GitHub directly](https://github.com/rs-station/rs-booster)