Hotfix/documentation (#254)

Documentation updates

Author: sabinem

.env.dist

@@ -0,0 +1,106 @@
+# ===========================================================
+# Environment variables for odtp
+# Setup options:
+# - [COMPOSE] `docker compose` (recommended)
+# - [DEV] `docker compose -f compose.dev.yml` (for development)
+# - [VM] server setup with poetry
+# ===========================================================
+
+# ===========================================================
+# Credentials with other services
+# - needed for all setup methods
+# ===========================================================
+
+# Credentials github
+# your github token
+GITHUB_TOKEN=
+
+# ===========================================================
+# Credentials that you can choose on setup
+# - needed for all setup methods
+# ===========================================================
+
+# Credentials S3
+ODTP_ACCESS_KEY=
+ODTP_SECRET_KEY=
+
+# mongodb user and password
+MONGO_DB_USER=
+MONGO_DB_PASSWORD=
+
+# mongoexpress user and password
+MONGO_EXPRESS_USER=
+MONGO_EXPRESS_PASSWORD=
+
+# ===========================================================
+# Database names
+# - needed for all setup methods
+# ===========================================================
+
+# odtp db instance in the mongo db: "odtp"
+ODTP_MONGO_DB=odtp
+
+# s3 bucket name: "odtp"
+ODTP_BUCKET_NAME=odtp
+
+# ===========================================================
+# ODTP Path is where the dashboard will store users,
+# digital twins and executions
+# - needed for all setup methods
+# ===========================================================
+
+# path where your executions run and the digital twins are stored
+ODTP_PATH=
+
+# ===========================================================
+# Volumes to persist database content
+# these must match path on your local computer
+# - only needed for setup methods [COMPOSE], [DEV]
+# ===========================================================
+
+# path where s3 data is stored
+MINIO_PATH=
+
+# path where mongodb content is stored
+MONGODB_PATH=
+
+# ===========================================================
+# Operational settings: change only if needed
+# - needed for all setup methods
+# ===========================================================
+
+# Dashboard parameters
+ODTP_DASHBOARD_PORT=8003
+ODTP_DASHBOARD_RELOAD=False
+
+# Log level
+ODTP_LOG_LEVEL=ERROR
+RUN_LOG_LEVEL=INFO
+
+# Set to False if your docker installation does not allow the flag --gpus all
+# Set to True in case you want to use GPUs
+ALLOW_DOCKER_GPUS=False
+
+# ===========================================================
+# Development settings: only needed for development
+# setup with compose.dev.yml:
+# `docker compose -f compose.dev.yml`
+# - only needed for setup method [DEV]
+# ===========================================================
+
+# Local path on your computer to your odtp installation
+APP_PATH=
+
+# Install the package in editable mode.
+PIP_INSTALL_ARGS="--editable"
+
+# ===========================================================
+# Service URLS
+# - only needed for setup method [VM]
+# ===========================================================
+
+# mongo url: example "mongodb://localhost:27017/"
+ODTP_MONGO_SERVER=
+
+# S3 server url: example: "https://s3.epfl.ch"
+ODTP_S3_SERVER=

.env.dist.compose

@@ -1,7 +1,7 @@
 __pycache__/
 .DS_Store
 .env*
-!.env.dist.*
+!.env.dist
 .nicegui
 .local
 odtp/odtp.log

.env.dist.compose.dev

@@ -13,7 +13,8 @@
     - gui: gui allows now to deprecate workflows, executions and component versions. Deprecated items are
     no longer offered in selects. Items can be deprecated and also reactivated
     - env: an additional env variable is added ALLOW_DOCKER_GPUS that must be set to false if the used Docker
-    version does not allow GPU settings such as 
+    version does not allow GPU settings such as `--gpus`
+
 - v0.4.0
     - gui: the general workflow for the user was improved (new Items are selected automatically for example)
     - gui: validation has been implemented in the forms to make sure data that is entered will be valid
@@ -46,7 +47,7 @@
     - hotfix ODTP port in docker compose
 
 - v0.2.6: Bugs correction
-    - Missing `ODTP_PATH` in `compose.yml`. 
+    - Missing `ODTP_PATH` in `compose.yml`.
 
 - v0.2.5: Bugs corrections and new features
     - Components tags parsing
@@ -60,22 +61,22 @@
 
 - v.0.2.3: Feature
     - Expose dashboard parameters: port and reload
-    
+
 - v.0.2.2: Bugs correction
     - Including submodules when cloning file
 
 - v.0.2.1: Add docker compose for easy setup
     - add compose.yml: it can be build with `docker compose up`
     - check `.env` file with `docker compose config`
-    - remove data mockup 
+    - remove data mockup
     - environment variables now loaded from the environment
 
 - v.0.2.0: Improvements in database and files management.
-    - New MongoDB Schema supporting users, digital twins, executions, and steps. 
+    - New MongoDB Schema supporting users, digital twins, executions, and steps.
     - Setup uses pyproject.toml and set up method changed to poetry
     - mongodb access function modified so that they can be used by both the GIU and the CLI
-    - CLI refactored with methods for creating and managing digital twins, and executions. 
-    - Automatic preparation of project folders for executions. 
+    - CLI refactored with methods for creating and managing digital twins, and executions.
+    - Automatic preparation of project folders for executions.
     - S3 uploading of outputs from each component.
     - Switch UI from Streamlit to Nicegui