Add almost-infinite scenario with Clark2Dt dispersal (#273)

Co-authored-by: Nicolás Firbas <nicolas.firbas@gmail.com>

* Sketch out Clark scenario code skeleton

* Implement Clark2Dt dispersal using inverse sampling

* Implement Clark2Dt self-dispersal probability using numerical integration

* Generalise Clark2Dt to p/=0 + add tests

* Make p=1 the default

* Merge spatially explicit scenario configs

* Merge the Clark2Dt scenario into the AlmostInfinite scenario

* Enable circle and rectangle origin sampling for both Normal and Clark2Dt dispersal in the AlmostInfinite scenario

* Switch to using cuda-toolkit action in CI

Author: juntyr

.github/workflows/ci.yml

@@ -22,14 +22,11 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install CUDA
-        run: |
-          wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
-          sudo mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600
-          curl -L -O https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-keyring_1.0-1_all.deb
-          sudo dpkg -i cuda-keyring_1.0-1_all.deb
-          sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
-          sudo apt-get update -q
-          sudo apt-get install cuda -y --no-install-recommends
+        uses: Jimver/cuda-toolkit@v0.2.14
+        with:
+          method: network
+          use-github-cache: false
+          use-local-cache: false
 
       - name: Install OpenMPI
         run: |
@@ -57,14 +54,11 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install CUDA
-        run: |
-          wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
-          sudo mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600
-          curl -L -O https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-keyring_1.0-1_all.deb
-          sudo dpkg -i cuda-keyring_1.0-1_all.deb
-          sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
-          sudo apt-get update -q
-          sudo apt-get install cuda -y --no-install-recommends
+        uses: Jimver/cuda-toolkit@v0.2.14
+        with:
+          method: network
+          use-github-cache: false
+          use-local-cache: false
 
       - name: Install OpenMPI
         run: |
@@ -99,14 +93,11 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install CUDA
-        run: |
-          wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
-          sudo mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600
-          curl -L -O https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-keyring_1.0-1_all.deb
-          sudo dpkg -i cuda-keyring_1.0-1_all.deb
-          sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
-          sudo apt-get update -q
-          sudo apt-get install cuda -y --no-install-recommends
+        uses: Jimver/cuda-toolkit@v0.2.14
+        with:
+          method: network
+          use-github-cache: false
+          use-local-cache: false
 
       - name: Install OpenMPI
         run: |

.github/workflows/coverage.yml

@@ -20,14 +20,11 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Install CUDA
-        run: |
-          wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
-          sudo mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600
-          curl -L -O https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-keyring_1.0-1_all.deb
-          sudo dpkg -i cuda-keyring_1.0-1_all.deb
-          sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
-          sudo apt-get update -q
-          sudo apt-get install cuda -y --no-install-recommends
+        uses: Jimver/cuda-toolkit@v0.2.14
+        with:
+          method: network
+          use-github-cache: false
+          use-local-cache: false
 
       - name: Install OpenMPI
         run: |

Cargo.lock

@@ -3,13 +3,13 @@
         /* selection of event log segments which will be analysed in the replay */
         segments: [
             /* a PathBuf which can contain Unix glob patterns
-            *  e.g. use "event_log / ** / *" (without spaces)
-            * where the event log was stored to the "event_log" directory */
+             *  e.g. use "event_log / ** / *" (without spaces)
+             * where the event log was stored to the "event_log" directory */
             (GlobPathBuf),
         ],
         /* in-memory buffering capacity of each log segment
-         * a higher capacity will batch up disk read calls but use more RAM */
-        /* optional, default = 100000 */
+         * a higher capacity will batch up disk read calls but use more RAM
+         * optional, default = 100000 */
         capacity: (0 < usize),
     ),