Merge branch 'release/0.16.0'

.devcontainer/Dockerfile

@@ -0,0 +1,26 @@
+# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.137.0/containers/java/.devcontainer/base.Dockerfile
+# 13 is not available
+ARG VARIANT="14"
+FROM mcr.microsoft.com/vscode/devcontainers/java:0-${VARIANT}
+
+# [Optional] Install Maven or Gradle
+ARG INSTALL_MAVEN="true"
+ARG MAVEN_VERSION=3.6.3
+ARG INSTALL_GRADLE="false"
+ARG GRADLE_VERSION=5.4.1
+RUN if [ "${INSTALL_MAVEN}" = "true" ]; then su vscode -c "source /usr/local/sdkman/bin/sdkman-init.sh && sdk install maven \"${MAVEN_VERSION}\""; fi \
+    && if [ "${INSTALL_GRADLE}" = "true" ]; then su vscode -c "source /usr/local/sdkman/bin/sdkman-init.sh && sdk install gradle \"${GRADLE_VERSION}\""; fi
+
+# [Optional] Install a version of Node.js using nvm for front end dev
+# ARG INSTALL_NODE="true"
+# ARG NODE_VERSION="lts/*"
+# RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "source /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# RUN mkdir /workspaces
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+# [Optional] Uncomment this line to install global node packages.
+# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g <your-package-here>" 2>&1

.devcontainer/devcontainer.json

@@ -0,0 +1,40 @@
+{
+    "name": "ckblib",
+    "build": {
+        "dockerfile": "Dockerfile",
+    },
+    "containerEnv": {
+        "GITHUB_TOKEN": "${localEnv:GITHUB_TOKEN}",
+        "GITHUB_USER": "${localEnv:GITHUB_USER}"
+    },
+    // Comment out the next line to run as root instead. Linux users,
+    // update Dockerfile with your user's UID/GID if not 1000.
+    // "runArgs": ["-u", "vscode"],
+    // In the container
+    // git clone into /workspaces by git clone https://github.com/dermatologist/dermml.git
+    // Increase password cache git config --global credential.helper 'cache --timeout=50600'
+    // "workspaceFolder": "/workspaces/dermml",
+    // "workspaceMount": "src=dermml,dst=/workspaces/dermml,type=volume,volume-driver=local",
+    // https://stackoverflow.com/questions/38520638/how-to-set-spring-profile-from-system-variable
+    // "runArgs": [ "-e", "SPRING_PROFILES_ACTIVE=dev"],
+    // Use 'settings' to set *default* container specific settings.json values on container create.
+    // You can edit these settings after create using File > Preferences > Settings > Remote.
+    "settings": {
+        "terminal.integrated.shell.linux": "/bin/bash"
+    },
+    // Uncomment the next line if you want to publish any ports.
+    // "appPort": [],
+    //"appPort": "8093:8080",
+    // Uncomment the next line to run commands after the container is created.
+    // "postCreateCommand": "java -version",
+    "shutdownAction": "none", // or stopContainer
+    "extensions": [
+        "vscjava.vscode-java-pack",
+        "redhat.vscode-xml",
+        "eamodio.gitlens",
+        "mhutchie.git-graph",
+        "humao.rest-client",
+        "Trinity.trinity",
+        "tht13.html-preview-vscode"
+    ]
+}

.gitignore

@@ -44,3 +44,4 @@ application/.factorypath
 library/.factorypath
 qtakes/.factorypath
 graph/.factorypath
+umls/.factorypath

CONTRIBUTING.md

@@ -0,0 +1,70 @@
+# How to contribute
+
+## Please note:
+
+* (Optional) We adopt [Git Flow](https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow). Most feature branches are pushed to the repository and deleted when merged to *develop* branch.
+* (**Important**): Submit pull requests to the *develop* branch or *feature/* branches
+* Use *GitHub Issues* for feature requests and bug reports. Include as much information as possible while reporting bugs.
+
+
+## Contributing (Step-by-step)
+
+1. [Fork the repo](http://help.github.com/fork-a-repo) and clone it to your local computer, and set up the upstream remote:
+
+        git clone https://github.com/YourGithubUsername/ckblib.git
+        cd ckblib
+        git remote add upstream https://github.com/dermatologist/ckblib.git
+
+2. Checkout out a new local branch based on your master and update it to the latest (BRANCH-123 is the branch name, You can name it whatever you want. Try to give it a meaningful name. If you are fixing an issue, please include the issue #).
+
+        git checkout -b BRANCH-123 develop
+        git clean -df
+        git pull --rebase upstream develop
+
+ > Please keep your code clean. If you find another bug, you want to fix while being in a new branch, please fix it in a separated branch instead.
+
+3. Push the branch to your fork. Treat it as a backup.
+
+        git push origin BRANCH-123
+
+4. Code
+
+  * Adhere to common conventions you see in the existing code.
+  * Include tests as much as possible, and ensure they pass.
+
+5. Commit to your branch
+
+         git commit -m "BRANCH-123: Put change summary here (can be a ticket title)"
+
+  **NEVER leave the commit message blank!** Provide a detailed, clear, and complete description of your commit!
+
+6. Update your branch to the latest code.
+
+        git pull --rebase upstream develop
+
+7. **Important** If you have made many commits, please squash them into atomic units of work. (Most Git GUIs such as sourcetree and smartgit offer a squash option)
+
+
+        git checkout develop
+        git pull --rebase upstream develop
+        git merge --squash BRANCH-123
+        git commit -m "fix: 123"
+
+  Push changes to your fork:
+
+        git push
+
+8. Issue a Pull Request
+
+  In order to make a pull request:
+  * Click "Pull Request".
+  * Choose the develop branch
+  * Click 'Create pull request'
+  * Fill in some details about your potential patch including a meaningful title.
+  * Click "Create pull request".
+
+  Thanks for that -- we'll get to your pull request ASAP. We love pull requests!
+
+## Feedback
+
+   If you need to contact me, see my contact details on my profile page.