-
Notifications
You must be signed in to change notification settings - Fork 24
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'master' of github.com:scalableminds/webknossos into emp…
…ty-list-drawings * 'master' of github.com:scalableminds/webknossos: (25 commits) Fix issues with styling in dark mode on login page (#7052) Fix nightly by setting missing token (#7048) Release 23.05.1 (#7042) DRY types in update_actions.ts (#7036) Remove some spammy logging from backend (#7039) Use zarr string fill values (#7017) Fix voxel offset for Neuroglancer Precomputed datasets (#7019) Log when user is activated (#7027) Fix exception in applying UpdateTreeGroupVisibility skeleton action (#7037) Fix organization storage layouting (#7034) Update docker compose commands + dev install readme (#7002) Add segment groups (#6966) Add screenshot nightly test for wkorg (#7030) Workaround for WebGL crash for datasets with many segmentation layers (#6995) Fix download of public annotation, include access ctx in user cache key (#7025) Fix that changing a segment color could lead to a crash (#7000) Add more error chaining to annotation download (#7023) Guard against NaNs in shader (#7018) Store editable mappings in multiple fossildb columns+keys (#6903) Context action to move tree to group (#7005) ...
- Loading branch information
Showing
158 changed files
with
4,285 additions
and
1,550 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,13 @@ | ||
| ## Development installation | ||
| ### Docker | ||
| This is only recommended for local testing. Docker 17+ and Docker Compose 1.18+ are required. | ||
| # Development installation | ||
|
|
||
| ## Docker | ||
|
|
||
| This is only recommended for local testing. Docker 19.03.0+ and Docker Compose 2.+ are required. | ||
|
|
||
| ```bash | ||
| git clone -b master --depth=1 [email protected]:scalableminds/webknossos.git | ||
| cd webknossos | ||
| docker-compose pull webknossos | ||
| docker compose pull webknossos | ||
| ./start-docker.sh | ||
| ``` | ||
|
|
||
|
|
@@ -16,7 +18,7 @@ See the wiki for [instructions on updating](https://github.com/scalableminds/web | |
|
|
||
| For non-localhost deployments, check out the [installation guide in the documentation](https://docs.webknossos.org/webknossos/installation.html). | ||
|
|
||
| ### Dependencies | ||
| ## Dependencies | ||
|
|
||
| * [Oracle JDK 11 to 14](http://www.oracle.com/technetwork/java/javase/downloads/index.html) or [Open JDK 11 to 14](http://openjdk.java.net/) (full JDK, JRE is not enough) | ||
| * [sbt](http://www.scala-sbt.org/) | ||
|
|
@@ -27,7 +29,10 @@ For non-localhost deployments, check out the [installation guide in the document | |
| * [yarn package manager](https://yarnpkg.com/) | ||
| * [git](http://git-scm.com/downloads) | ||
|
|
||
| ### MacOS | ||
| * For some development tasks like refreshing snapshots, Docker 19.03.0+ and Docker Compose 2.+ are required | ||
|
|
||
| ## MacOS | ||
|
|
||
| ```bash | ||
| # WEBKNOSSOS needs to be run from x86_64 environment (only applicable for arm64-based Macs) | ||
| arch -x86_64 /bin/zsh | ||
|
|
@@ -60,80 +65,90 @@ psql -c "GRANT ALL PRIVILEGES ON DATABASE webknossos TO postgres;" | |
|
|
||
| # Checkout the WEBKNOSSOS git repository | ||
| git clone [email protected]:scalableminds/webknossos.git | ||
|
|
||
|
|
||
| ``` | ||
|
|
||
| Note: On arm64-based Macs (e.g. M1), you need to run WEBKNOSSOS in an x86_64 environment (Rosetta 2). In case you accidentally started WEBKNOSSOS in an arm64 environment, it is advisable to delete several caches `~/.m2`, `~/ivy2`, `~/.sbt`, `~/.yarn-cache` and run `./clean`. Since Postgres and Redis are isolated processes, they can be run either from arm64 or x86_64 environments. | ||
|
|
||
|
|
||
| ### Ubuntu 20.04 LTS | ||
| ## Ubuntu 22.04 LTS | ||
|
|
||
| ```bash | ||
| sudo apt install -y curl ca-certificates wget | ||
| # Adding repositories for nodejs, sbt and yarn | ||
| curl -fsSL https://deb.nodesource.com/setup_lts.x | sudo -E bash - | ||
| echo "deb https://repo.scala-sbt.org/scalasbt/debian all main" | sudo tee /etc/apt/sources.list.d/sbt.list | ||
| echo "deb https://repo.scala-sbt.org/scalasbt/debian /" | sudo tee /etc/apt/sources.list.d/sbt_old.list | ||
| curl -sL "https://keyserver.ubuntu.com/pks/lookup?op=get&search=0x2EE0EA64E40A89B84B2DF73499E82A75642AC823" | sudo apt-key add | ||
| curl -sL "https://keyserver.ubuntu.com/pks/lookup?op=get&search=0x2EE0EA64E40A89B84B2DF73499E82A75642AC823" | sudo -H gpg --no-default-keyring --keyring gnupg-ring:/etc/apt/trusted.gpg.d/scalasbt-release.gpg --import | ||
| sudo chmod 644 /etc/apt/trusted.gpg.d/scalasbt-release.gpg | ||
| curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | sudo apt-key add - | ||
| echo "deb https://dl.yarnpkg.com/debian/ stable main" | sudo tee /etc/apt/sources.list.d/yarn.list | ||
|
|
||
| sudo apt update | ||
| sudo apt install -y nodejs git postgresql postgresql-client scala sbt openjdk-14-jdk yarn redis-server build-essential libblosc1 | ||
| sudo apt install -y nodejs git postgresql postgresql-client scala sbt openjdk-11-jdk yarn redis-server build-essential libblosc1 | ||
|
|
||
| # Assign a password to PostgreSQL user | ||
| sudo -u postgres psql -c "ALTER USER postgres WITH ENCRYPTED PASSWORD 'postgres';" | ||
| # Clone the git repo to the current directory | ||
| git clone -b master --depth=1 https://github.com/scalableminds/webknossos.git | ||
| ``` | ||
|
|
||
| If you already have a different Java version installed, set the default version to Java 14: | ||
| - run `sudo update-alternatives --config java` | ||
| - when prompted, select the desired version | ||
| If you already have a different Java version installed, set the default version to Java 11: | ||
|
|
||
| * run `sudo update-alternatives --config java` | ||
| * when prompted, select the desired version | ||
|
|
||
| On older Ubuntu distributions: Please make sure to have the correct versions of node, PostgreSQL and java installed. | ||
|
|
||
| ### Manual Installation | ||
| ## Manual Installation | ||
|
|
||
| ### Java | ||
|
|
||
| ##### Java | ||
| * Install Java JDK 14 (from Oracle or OpenJDK) | ||
| * make sure `JAVA_HOME` and `JDK_HOME` are set and `PATH` contains the path to JDK | ||
|
|
||
| ##### sbt | ||
| See: http://www.scala-sbt.org/release/docs/Getting-Started/Setup.html | ||
| ### sbt | ||
|
|
||
| * See: [http://www.scala-sbt.org/release/docs/Getting-Started/Setup.html](http://www.scala-sbt.org/release/docs/Getting-Started/Setup.html) | ||
|
|
||
| ##### PostgreSQL | ||
| * Install PostgreSQL from https://www.postgresql.org/download/ | ||
| ### PostgreSQL | ||
|
|
||
| * Install PostgreSQL from [https://www.postgresql.org/download/](https://www.postgresql.org/download/) | ||
| * PostgreSQL version **10+ is required** | ||
|
|
||
| ##### Redis | ||
| * Install Redis from https://redis.io/download | ||
| ### Redis | ||
|
|
||
| * Install Redis from [https://redis.io/download](https://redis.io/download) | ||
|
|
||
| ### node.js & yarn | ||
|
|
||
| ##### node.js & yarn | ||
| * Install node from http://nodejs.org/download/ | ||
| * Install node from [http://nodejs.org/download/](http://nodejs.org/download/) | ||
| * node version **16+ is required** | ||
| * Install yarn package manager: `npm install -g yarn` | ||
|
|
||
| ### Run locally | ||
| ## Run locally | ||
|
|
||
| First, install all frontend dependencies via | ||
|
|
||
| ```bash | ||
| yarn install | ||
| ``` | ||
|
|
||
| Note: During this installation step, it might happen that the module `gl` cannot be installed correctly. As this module is only used for testing WEBKNOSSOS, you can safely ignore this error. | ||
|
|
||
| To start WEBKNOSSOS, use | ||
|
|
||
| ```bash | ||
| yarn start | ||
| ``` | ||
|
|
||
| This will fetch all Scala, Java and node dependencies and run the application on Port 9000. | ||
| Make sure that the PostgreSQL and Redis services are running before you start the application. | ||
|
|
||
| ## Upgrades | ||
|
|
||
| For upgrades, please check the [changelog](CHANGELOG.released.md) & [migration guide](MIGRATIONS.released.md). | ||
|
|
||
| ## Tests | ||
|
|
||
| ```bash | ||
| # Frontend linting | ||
| yarn run lint | ||
|
|
@@ -151,5 +166,5 @@ yarn flow | |
| yarn test-verbose | ||
|
|
||
| # End-to-end tests | ||
| docker-compose run e2e-tests | ||
| docker compose run e2e-tests | ||
| ``` | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.