v0.0.5 release

.gitattributes

@@ -1,2 +0,0 @@
-*.txt filter=lfs diff=lfs merge=lfs -text
-*.mci filter=lfs diff=lfs merge=lfs -text

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,39 @@
+---
+name: 🐛 Bug report
+about: If something isn't working 🔧
+title: ''
+labels: bug
+assignees:
+---
+
+## 🐛 Bug Report
+
+<!-- A clear and concise description of what the bug is. -->
+
+## 🔬 How To Reproduce
+
+Steps to reproduce the behavior:
+
+1. ...
+
+### Code sample
+
+<!-- If applicable, attach a minimal code sample to reproduce the decried issue. -->
+
+### Environment
+
+* OS: [e.g. Linux / Windows / macOS]
+* CMake version: [e.g. 3.28.6]
+* Compiler: [e.g. GNU, Clang]
+
+### Screenshots
+
+<!-- If applicable, add screenshots to help explain your problem. -->
+
+## 📈 Expected behavior
+
+<!-- A clear and concise description of what you expected to happen. -->
+
+## 📎 Additional context
+
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,3 @@
+# Configuration: https://help.github.com/en/github/building-a-strong-community/configuring-issue-templates-for-your-repository
+
+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,23 @@
+---
+name: 🚀 Feature request
+about: Suggest an idea for this project 🏖
+title: ''
+labels: enhancement
+assignees:
+---
+
+## 🚀 Feature Request
+
+<!-- A clear and concise description of the feature proposal. -->
+
+## 🔈 Motivation
+
+<!-- Please describe the motivation for this proposal. -->
+
+## 🛰 Alternatives
+
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
+
+## 📎 Additional context
+
+<!-- Add any other context or screenshots about the feature request here. -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,27 @@
+## Description
+
+<!-- Add a more detailed description of the changes if needed. -->
+
+## Related Issue
+
+<!-- If your PR refers to a related issue, link it here. -->
+
+## Type of Change
+
+<!-- Mark with an `x` all the checkboxes that apply (like `[x]`) -->
+
+- [ ] 📚 Examples / docs / tutorials / dependencies update
+- [ ] 🔧 Bug fix (non-breaking change which fixes an issue)
+- [ ] 🥂 Improvement (non-breaking change which improves an existing feature)
+- [ ] 🚀 New feature (non-breaking change which adds functionality)
+- [ ] 💥 Breaking change (fix or feature that would cause existing functionality to change)
+- [ ] 🔐 Security fix
+
+## Checklist
+
+<!-- Mark with an `x` all the checkboxes that apply (like `[x]`) -->
+
+- [ ] I've read the `CODE_OF_CONDUCT.md` document.
+- [ ] I've updated the code style using the `pre-commit hooks`.
+- [ ] I've written tests for all new methods and classes that I created.
+- [ ] I've written the docstring for all the methods and classes that I used.

.github/release-drafter.yml

@@ -0,0 +1,31 @@
+name-template: 'v$RESOLVED_VERSION 🌈'
+tag-template: 'v$RESOLVED_VERSION'
+categories:
+  - title: '🚀 Features'
+    labels:
+      - 'feature'
+      - 'enhancement'
+  - title: '🐛 Bug Fixes'
+    labels:
+      - 'fix'
+      - 'bugfix'
+      - 'bug'
+  - title: '🧰 Maintenance'
+    label: 'chore'
+change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
+change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
+version-resolver:
+  major:
+    labels:
+      - 'major'
+  minor:
+    labels:
+      - 'minor'
+  patch:
+    labels:
+      - 'patch'
+  default: patch
+template: |
+  ## Changes
+
+  $CHANGES

.github/stale.yml

@@ -0,0 +1,17 @@
+# Number of days of inactivity before an issue becomes stale
+daysUntilStale: 60
+# Number of days of inactivity before a stale issue is closed
+daysUntilClose: 7
+# Issues with these labels will never be considered stale
+exemptLabels:
+  - pinned
+  - security
+# Label to use when marking an issue as stale
+staleLabel: wontfix
+# Comment to post when marking an issue as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. It will be closed if no further activity occurs. Thank you
+  for your contributions.
+# Comment to post when closing a stale issue. Set to `false` to disable
+closeComment: false

.github/workflows/build.yml

@@ -0,0 +1,26 @@
+name: Build, Test & Install
+
+permissions:
+  contents: read
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    types: [opened, reopened, synchronize]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [self-hosted]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - name: Checkout project
+      uses: actions/checkout@v4.1.7
+    - name: Build & install
+      run: |
+        docker build -t mcml:github .

.github/workflows/greetings.yml

@@ -0,0 +1,21 @@
+name: Greetings
+
+on: [pull_request, issues]
+
+permissions:
+  contents: read
+  issues: write
+  pull-requests: write
+
+jobs:
+  greeting:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/first-interaction@v1
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        pr-message:  'Hello @${{ github.actor }}, thank you for submitting a PR! We will respond as soon as possible.'
+        issue-message: |
+          Hello @${{ github.actor }}, thank you for your interest in our work!
+
+          If this is a bug report, please provide screenshots and **minimum viable code to reproduce your issue**, otherwise we can not help you.

.github/workflows/release-drafter.yml

@@ -0,0 +1,41 @@
+name: Release Drafter
+
+on:
+  push:
+    # branches to consider in the event; optional, defaults to all
+    branches:
+      - main
+  # pull_request event is required only for autolabeler
+  pull_request:
+    # Only following types are handled by the action, but one can default to all as well
+    types: [opened, reopened, synchronize]
+  # pull_request_target event is required for autolabeler to support PRs from forks
+  # pull_request_target:
+  #   types: [opened, reopened, synchronize]
+
+permissions:
+  contents: read
+
+jobs:
+  update_release_draft:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
+      # write permission is required for autolabeler
+      # otherwise, read permission is required at least
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      # (Optional) GitHub Enterprise requires GHE_HOST variable set
+      #- name: Set GHE_HOST
+      #  run: |
+      #    echo "GHE_HOST=${GITHUB_SERVER_URL##https:\/\/}" >> $GITHUB_ENV
+
+      # Drafts your next Release notes as Pull Requests are merged into "master"
+      - uses: release-drafter/release-drafter@v6
+        # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml
+        # with:
+        #   config-name: my-config.yml
+        #   disable-autolabeler: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -11,3 +11,4 @@
 cutil-linux
 executable
 *build*
+*.cast

.gitlab-ci.yml

@@ -13,6 +13,8 @@ build:
     - mkdir cmake-build && cd cmake-build
     - cmake ..
     - make MCML -j
+    - make package -j
+    - dpkg -i MCML*.deb
   artifacts:
     paths:
       - cmake-build/

CHANGELOG.md

@@ -10,55 +10,59 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
--
+- Adds Cpack to CMake to package .deb file
+- Adds citation file.
+- Adds GitHub actions, templates, etc.
+- Adds logo.
 
 ### Changed
 
--
+- Improves information on how to build the application.
+- Integrates CLI11 as a argument parser.
 
 ### Removed
 
 -
 
 ### Fixed
 
--
+- Fixes illegal memory access for large numbers of simulations.
 
 ## [0.0.4]
 
 ### Added
 - Added new macro definition for CUDA_SAFE_CALL_INFO to print additional information when an error occurs.
-  (https://git.dkfz.de/imsy/issi/mcmlgpu/-/commit/b957acc240fd0b014c1136b13811d7ec260fccdd)
+  (b957acc240fd0b014c1136b13811d7ec260fccdd)
 - MCML now expects an MCO file instead of an MCO FOLDER as input.
-  (https://git.dkfz.de/imsy/issi/mcmlgpu/-/commit/9689ad1fab47407d5fe649677420f9e1fd35c561)
+  (9689ad1fab47407d5fe649677420f9e1fd35c561)
 - Added conan package
-  (https://git.dkfz.de/imsy/issi/mcmlgpu/-/commit/a5573e170f1795ca3dfb523386557649e509a545)
+  (a5573e170f1795ca3dfb523386557649e509a545)
 - Adds editor config and pre-commit hooks
 - Added `-V` flag to print software version and build information
 
 ### Changed
 - Modified path for safe_primes installation to the same path as MCML
-  (https://git.dkfz.de/imsy/issi/mcmlgpu/-/commit/c310827b19735bb81cd6c9ed08d3a82acbd5feff)
+  (c310827b19735bb81cd6c9ed08d3a82acbd5feff)
 - Defined path to safeprimes relative to the executable path
-  (https://git.dkfz.de/imsy/issi/mcmlgpu/-/commit/91759c9207f714db4274bf5a2499684b7dce8a36)
+  (91759c9207f714db4274bf5a2499684b7dce8a36)
 
 ### Removed
 - Removed elapsed time computation as it was not used anymore.
-  (https://git.dkfz.de/imsy/issi/mcmlgpu/-/commit/b957acc240fd0b014c1136b13811d7ec260fccdd)
+  (b957acc240fd0b014c1136b13811d7ec260fccdd)
 - Removed deprecated information from README.md
-  (https://git.dkfz.de/imsy/issi/mcmlgpu/-/commit/85ada768be4a3fc447726294912af4da619c9390)
+  (85ada768be4a3fc447726294912af4da619c9390)
 - Removed dependency from the definition of __CUDA_ARCH__
-  (https://git.dkfz.de/imsy/issi/mcmlgpu/-/commit/078ef4a7e0a62585347baa2c3677177b234eb26b)
+  (078ef4a7e0a62585347baa2c3677177b234eb26b)
 - Removed unused include statements.
-  (https://git.dkfz.de/imsy/issi/mcmlgpu/-/commit/078ef4a7e0a62585347baa2c3677177b234eb26b)
+  (078ef4a7e0a62585347baa2c3677177b234eb26b)
 
 ### Fixed
 - Fixed an issue of illegal memory access by removing duplicated memory allocation for the number of photons left in the
-  host state struct (https://git.dkfz.de/imsy/issi/mcmlgpu/-/commit/1eb40b22e0828ddc43ac55a5b9eee01c22d4ea08)
+  host state struct (1eb40b22e0828ddc43ac55a5b9eee01c22d4ea08)
 - Fixed path to safeprimes in init_RNG
-  (https://git.dkfz.de/imsy/issi/mcmlgpu/-/commit/ad34a281cc74303134c07421024bb5e3a53995b2)
+  (ad34a281cc74303134c07421024bb5e3a53995b2)
 - Fixed penetration depth calculations (issue #13).
-  (https://git.dkfz.de/imsy/issi/mcmlgpu/-/commit/a0c99b3b8d2659a07324dbef73cafe0b4602e005)
+  (a0c99b3b8d2659a07324dbef73cafe0b4602e005)
 
 ## [v0.0.3]
 

CITATION.cff

@@ -0,0 +1,13 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Ayala"
+  given-names: "Leonardo"
+  orcid: "https://orcid.org/0000-0002-3574-2085"
+- family-names: "Maier-Hein"
+  given-names: "Lena"
+  orcid: "https://orcid.org/0000-0003-4910-9368"
+title: "mcmlgpu"
+version: 0.0.4
+url: "https://github.com/IMSY-DKFZ/mcmlgpu"
+doi: 10.5281/zenodo.13304909