Xmipp Release Procedures

This document describes how to manage versions following semantic version standar , and releases for the different components of the Xmipp ecosystem: xmipp3-installer, scipion-em-xmipp, xmipp3, xmippCore and xmippViz.

Fig. 1 Repositories dependencies

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Repository	Steps to Create a New Version
xmipp3-installer	Trigger GitHub manual action Uploads automatically to PyPI Scipion-em-xmipp installs it via requirements.txt xmipp3-installer==1.*
scipion-em-xmipp	Update changelog.md Update version in xmipp3/version.py (__version__) If Xmipp major version changes: update _binVersion and _binTagVersion Trigger GitHub Release action → uploads to PyPI and creates tag
xmipp3	Edit xmipp/version-info.json: version_number, release_date Edit version_name only if major changes Update dependency versions for xmippCore / xmippViz if major changes Update changelog.md Trigger GitHub Release action → creates tag and release
xmippCore	Add new version and changes in changeLOG.md Trigger GitHub Release action → creates new tag
xmippViz	Add new version and changes in changeLOG.md Trigger GitHub Release action → creates new tag

xmipp3-installer 🗃️

xmipp3-installer packages the Xmipp binaries and is published on PyPI. It is automatically installed by the Scipion plugin scipion-em-xmipp.

Release Generation

Releases are produced via the GitHub manual action Generate release (Pypi, tag, & GitHub Release). Executing this action will upload a new version to PyPI and create the corresponding Git tag and GitHub Release.

Installation Through Scipion

The scipion-em-xmipp plugin installs it using its requirements.txt:

xmipp3-installer==1.*

scipion-em-xmipp 🗃️

This is the Scipion plugin that integrates Xmipp into Scipion.

Steps to Create a New Release

1. Update the changelog

   Edit changelog.md with the new version and a list of changes.

2. Update the version

   Modify the __version__ variable in:

   scipion-em-xmipp/xmipp3/version.py
   

3. Run the GitHub Release action

   Trigger the manual action Release. This will upload the new version to PyPI and create a new Git tag and GitHub Release.

Major Xmipp Version Changes

If the major version of Xmipp changes, update these fields:

scipion-em-xmipp/xmipp3/version.py
    _binVersion
    _binTagVersion

Use the Protein cataloge for Xmipp releases name

xmipp3 🗃️

Top-level Xmipp distribution, bundling submodules such as xmippCore and xmippViz.

Version Updates

Edit the version information in:

xmipp/version-info.json

The fields to modify are:

• version_number

• version_name: only when the major version changes. Use the Protein cataloge for Xmipp releases name

• release_date

If xmippCore or xmippViz increase their major version, update their version references inside version-info.json.

Release Procedure

1. Update changelog.md with the new version and changes.

2. Trigger the GitHub manual action Release to Create a new Git tag and Publish a GitHub Release

xmippCore 🗃️

Core Xmipp libraries and algorithms.

Steps to Create a New Release

1. Add a new section in changeLOG.md including Version number and Description of changes

2. Trigger the Release GitHub manual action to generate a new Git tag

xmippViz 🗃️

Visualization module for Xmipp and Scipion

Steps to Create a New Release

1. Add the new version and changes to changeLOG.md including Version number and Description of changes

2. Execute the GitHub manual action Release to create the new tag

🧬 Protein Catalog for Xmipp releases naming 🧬

A

Actin – Cell structure and movement

Apoferritin – Iron storage scaffold protein

ATP synthase – Produces ATP from ADP

B

Bacteriorhodopsin – Light-driven proton pump

Beta-tubulin – Microtubule structural protein

Biotin carboxylase – Catalyzes carboxylation reactions

C

Cas9 – DNA cutting enzyme

CFTR – Chloride ion channel

Clathrin – Vesicle formation protein

D

Dynein – Moves cargo along microtubules

DNA polymerase – DNA replication enzyme

Dicer – Processes microRNA precursors

E

Elastin – Provides tissue elasticity

Electron transfer flavoprotein – Transfers electrons in mitochondria

Elongation factor 2 – Assists protein translation

F

Ferritin – Iron storage protein

Fibrinogen – Blood clot formation

Flagellin – Builds bacterial flagella

G

GAPDH – Glycolysis enzyme

GroEL – Protein folding chaperone

GPCR – Signal reception and transduction

H

Hemoglobin – Oxygen transport

Histone – DNA packaging protein

Hsp90 – Protein folding chaperone

I

Integrin – Cell adhesion receptor

Immunoglobulin G – Antibody immune defense

Ion channel TRPV1 – Heat/pain sensor channel

K

Keratin – Structural hair/nail protein

Kinesin – Microtubule cargo transport

Kinase (PKA) – Phosphorylates target proteins

L

Lactate dehydrogenase – Converts lactate to pyruvate

Laminin – Extracellular matrix structural protein

Lipase – Breaks down fats

M

Myosin – Motor protein for movement

Myoglobin – Oxygen storage in muscles

Mitochondrial complex I – Electron transport in mitochondria

N

NADH dehydrogenase – Oxidizes NADH in mitochondria

Na⁺/K⁺-ATPase – Maintains ion gradients

Nucleosome – DNA wound around histones

O

Opsin – Light-detecting protein

Outer membrane porin – Small molecule transport

Oxytocin – Hormone, induces contractions

P

p53 – Tumor suppressor

Photosystem II – Splits water in photosynthesis

Proteasome – Degrades unwanted proteins

R

Ribosome – Protein synthesis machine

RNA polymerase II – Transcribes mRNA

Rubisco – Fixes carbon dioxide

S

Spike (SARS-CoV-2) – Virus entry protein

Sec61 translocon – Inserts proteins into ER

Synapsin – Regulates neurotransmitter release

T

Tubulin – Microtubule building block

Troponin – Regulates muscle contraction

TRPV1 – Heat/pain sensory channel

U

Ubiquitin – Marks proteins for degradation

Urease – Breaks down urea

Uncoupling protein – Dissipates mitochondrial proton gradient

V

V-ATPase – Acidifies organelles

Vinculin – Connects cytoskeleton to membrane

Voltage-gated sodium channel – Action potential initiation

W

Wnt protein – Cell signaling and development

Wee1 kinase – Controls cell cycle

Wilms tumor protein (WT1) – Kidney development regulator

Y

YAP – Transcription coactivator, growth

Y-box binding protein – Regulates transcription and translation

Z

Zinc finger protein – DNA binding protein

ZO-1 – Tight junction scaffolding