Merge branch 'develop' into main

.github/ISSUE_TEMPLATE/issue_report.yml

@@ -0,0 +1,101 @@
+name: Issue Report
+description: Report a bug, ask for support or make feature request
+title: "Put issue title here"
+labels: ["pending"]
+body:
+  - type: dropdown
+    id: issue-type
+    attributes:
+      label: Issue type
+      description: What type of issue would you like to report?
+      multiple: false
+      options:
+        - Bug
+        - Build/Install
+        - Performance
+        - Support
+        - Feature Request
+        - Documentation Feature Request
+        - Documentation Bug
+        - Others
+    validations:
+      required: true
+  - type: dropdown
+    id: tomobear-source
+    attributes:
+      label: TomoBEAR source
+      description: TomoBEAR is used from
+      multiple: true
+      options:
+        - source code (via interactive MATLAB session)
+        - standalone binary (using MATLAB libraries)
+    validations:
+      required: true
+  - type: input
+    id: tomobear-version
+    attributes:
+      label: TomoBEAR version
+      description: Which TomoBEAR version do you use? 
+      placeholder: v0.4.0
+    validations:
+      required: true
+  - type: markdown
+    attributes:
+      value: |
+        If you cloned specific branch or commit, please execute "git log --pretty="%H - %cd" -n 1" in your cloned TomoBEAR source code folder and put its output in the field above
+  
+  - type: dropdown
+    id: computing-system
+    attributes:
+      label: Computing system
+      description: Which kind of computing system(s) do you use?
+      multiple: true
+      options:
+        - Standalone GPU workstation
+        - HPC cluster (interactive computing node)
+        - HPC cluster (via scheduler submission)
+    validations:
+      required: true
+
+  - type: textarea
+    id: issue-description
+    attributes:
+      label: Issue description
+      description: Provide a clear description of what happend and what did you expect to happen.
+      placeholder: Tell us what you see!
+    validations:
+      required: true
+  - type: textarea
+    id: configs
+    attributes:
+      label: Input configuration (JSON) file
+      description: Please copy and paste your input configuration (JSON) file. Use 
+      value: "```JSON { ... } ```"
+    validations:
+      required: true
+
+  - type: textarea
+    id: additional-info
+    attributes:
+      label: Additional info
+      description: Add any other context about the problem here (actions to reproduce, log/error messages, example data, additional configurations, screenshots, links/references).
+
+  - type: input
+    id: gpu-info
+    attributes:
+      label: GPU model and memory 
+      description: if the problem might be related to the GPU parallelization 
+      placeholder: NVIDIA Ampere A40-48GB
+  - type: input
+    id: cuda-info
+    attributes:
+      label: CUDA version(s)
+      description: if the problem might be related to the GPU parallelization 
+      placeholder: CUDA-11.5
+
+  - type: textarea
+    id: software-info
+    attributes:
+      label: Software setup 
+      description: Give here list of software and their versions (and other relevant info) which may be related to the issue (e.g. MATLAB, IMOD, Dynamo, MotionCor2, AreTomo, Gctf, IsoNet, etc.)   
+      placeholder: MATLAB-2021a, IMOD-4.11.24; Gctf-v1.18; etc.

AUTHORS.md

@@ -1,16 +1,13 @@
 ## TomoBEAR authors
 
-Max Delbruck Center for Molecular Medicine, Berlin, Germany (<https://www.mdc-berlin.de>)
+Copyright (c) 2022 Max Delbruck Center for Molecular Medicine, Berlin, Germany (<https://www.mdc-berlin.de>)
 
 * Mikhail Kudryashev - project leader
 * Artsemi Yushkevich - developer
 * Vasilii Mikirtumov - application engineer
 
+Copyright (c) 2021 Max Planck Institute of Biophysics, Frankfurt (Hesse), Germany (<https://www.biophys.mpg.de/en>)
 
-Max Planck Institute of Biophysics, Frankfurt (Hesse), Germany (<https://www.biophys.mpg.de/en>)
-
+* Mikhail Kudryashev - project leader
 * Nikita Balyschew - core version developer
-
-## External modified software authors
-
-TomoBEAR also contains modified pieces of MATLAB source code of the Dynamo package developed by D. Castaño-Díez et al.: https://www.dynamo-em.org.
+* Vasilii Mikirtumov - application engineer

CHANGELOG.md

@@ -2,6 +2,30 @@
 
 All notable changes will be documented in this file.
 
+## v0.4.0 - 2023-08-07
+
+### :rocket: New Features
+* ```crYOLO``` - module wrapping [crYOLO](https://cryolo.readthedocs.io/en/stable/index.html) - DL tool, based on **You Only Look Once (YOLO)** object detection system for predicting particle coordinates (basically picking them) in cryo-electron tomograms
+
+### :arrow_up: Improvements
+* ```IsoNet```: added possibility to post-process IsoNet-corrected tomograms using NAD filtering
+* ```DynamoTemplateMatching```: enabled usage of the tomograms from the custom user-provided path
+* ```AreTomo```:
+  * enabled direct usage of AreTomo alignment parameters from previously executed AreTomo step
+  * enabled parameters: tilt axis offset (pre-tilt) and temporary reconstruction thickness (VolZ)
+
+### :bug: Important fixes
+* ```DynamoTemplateMatching```: fixed bug preventing GPU-enabled speedup
+
+### :exclamation: Important updates
+* **changed license** of the core code base from [`AGPLv3`](https://www.gnu.org/licenses/agpl-3.0.en.html) to [`GPLv3`](https://www.gnu.org/licenses/gpl-3.0.en.html) - changed license to a bit more permissive version in order to allow software maintainers and other TomoBEAR contributors more flexibility in terms of TomoBEAR modifications, needed to provide a TomoBEAR operation over local networks (like institutional intranets and/or shared filesystems);
+* **updated documentation**:
+  * recorded a [set of short 8-12 min video-tutorials](https://www.youtube.com/watch?v=2uizkE616tE&list=PLdMU06ILLrYKjI-Z0qezcNheEtpVulMao&pp=iAQB) on TomoBEAR installation and 80S ribosome (EMPIAR-10064) tutorial;
+  * added [contribution guidelines and tips](https://github.com/KudryashevLab/TomoBEAR/blob/main/CONTRIBUTING.md)
+  * extended ["Usage"](https://github.com/KudryashevLab/TomoBEAR/wiki/Usage) and reviewed ["Installation and Setup"](https://github.com/KudryashevLab/TomoBEAR/wiki/Installation-and-Setup) sections;
+  * added ["External Software"](https://github.com/KudryashevLab/TomoBEAR/wiki/External-Software) section for dependencies installation/citation description.
+
+---
 ## v0.3.0 - 2023-05-22
 
 ### :rocket: New Features

CITATION.cff

@@ -20,6 +20,6 @@ authors:
     given-names: Misha
     orcid: https://orcid.org/0000-0003-3550-6274
 title: "Streamlined Structure Determination by Cryo-Electron Tomography and Subtomogram Averaging using TomoBEAR"
-version: 0.3.0
+version: 0.4.0
 doi: https://doi.org/10.1101/2023.01.10.523437
-date-released: 2023-05-22
+date-released: 2023-08-07