v3.1.0

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: astral-sh/setup-uv@v5
-      - run: uv sync
+      - run: uv sync --frozen
       - run: uv run ruff check .
       - run: uv run ruff format --check .
       - run: uv run mypy app
@@ -41,6 +41,6 @@ jobs:
       - uses: astral-sh/setup-uv@v5
       - uses: actions/setup-node@v4
         with: { node-version: 22, cache: npm, cache-dependency-path: frontend/package-lock.json }
-      - run: cd backend && uv sync && (uv run uvicorn app.main:app --port 8000 &)
+      - run: cd backend && uv sync --frozen && (uv run uvicorn app.main:app --port 8000 &)
       - run: cd frontend && npm ci && npx playwright install --with-deps chromium
       - run: cd frontend && npm run test:e2e

.serena/project.yml

@@ -1,43 +1,6 @@
-# the name by which the project can be referenced within Serena
+# the name by which the project can be referenced within Serena/when chatting with the LLM.
 project_name: "Arena3Dweb"
 
-
-# list of languages for which language servers are started; choose from:
-#   al                  angular             ansible             bash                clojure
-#   cpp                 cpp_ccls            crystal             csharp              csharp_omnisharp
-#   dart                elixir              elm                 erlang              fortran
-#   fsharp              go                  groovy              haskell             haxe
-#   hlsl                html                java                json                julia
-#   kotlin              lean4               lua                 luau                markdown
-#   matlab              msl                 nix                 ocaml               pascal
-#   perl                php                 php_phpactor        powershell          python
-#   python_jedi         python_ty           r                   rego                ruby
-#   ruby_solargraph     rust                scala               scss                solidity
-#   svelte              swift               systemverilog       terraform           toml
-#   typescript          typescript_vts      vue                 yaml                zig
-#   (This list may be outdated. For the current list, see values of Language enum here:
-#   https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py
-#   For some languages, there are alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.)
-# Note:
-#   - For C, use cpp
-#   - For JavaScript, use typescript
-#   - For Angular projects, use angular (subsumes typescript+html; requires `npm install` in the project root)
-#   - For Svelte projects, use svelte (subsumes typescript/javascript for .svelte projects; requires npm)
-#   - For SCSS / Sass / plain CSS, use scss (some-sass-language-server handles all three)
-#   - For Free Pascal/Lazarus, use pascal
-# Special requirements:
-#   Some languages require additional setup/installations.
-#   See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers
-# When using multiple languages, the first language server that supports a given file will be used for that file.
-# The first language is the default language and the respective language server will be used as a fallback.
-# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored.
-# R dropped: legacy code being deleted through the v3 migration, and its LSP
-# (R `languageserver` package) isn't installed — its failure aborted the whole
-# language-server manager. Active dev is TS (frontend) + Python (backend).
-languages:
-- typescript
-- python
-
 # the encoding used by text files in the project
 # For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings
 encoding: "utf-8"
@@ -59,23 +22,19 @@ ignore_all_files_in_gitignore: true
 
 # advanced configuration option allowing to configure language server-specific options.
 # Maps the language key to the options.
-# Have a look at the docstring of the constructors of the LS implementations within solidlsp (e.g., for C# or PHP) to see which options are available.
-# No documentation on options means no options are available.
+# The settings are considered only if the project is trusted (see global configuration to define trusted projects).
+# See https://oraios.github.io/serena/02-usage/050_configuration.html#language-server-specific-settings
 ls_specific_settings: {}
 
-# list of additional workspace folder paths for cross-package reference support (e.g. in monorepos).
-# Paths can be absolute or relative to the project root.
-# Each folder is registered as an LSP workspace folder, enabling language servers to discover
-# symbols and references across package boundaries.
-# Currently supported for: TypeScript.
-# Example:
-#   additional_workspace_folders:
-#     - ../sibling-package
-#     - ../shared-lib
-additional_workspace_folders: []
-
 # list of additional paths to ignore in this project.
 # Same syntax as gitignore, so you can use * and **.
+# Important: quote patterns that start with `*`, otherwise YAML treats them as aliases.
+# Example:
+#   ignored_paths:
+#     - "examples/**"
+#     - ".worktrees/**"
+#     - "**/bin/**"
+#     - "**/obj/**"
 # Note: global ignored_paths from serena_config.yml are also applied additively.
 ignored_paths: []
 
@@ -135,3 +94,75 @@ read_only_memory_patterns: []
 # Extends the list from the global configuration, merging the two lists.
 # Example: ["_archive/.*", "_episodes/.*"]
 ignored_memory_patterns: []
+
+# list of additional workspace folder paths for cross-package reference support.
+# Paths can be absolute or relative to the project root.
+# Each folder is registered as an LSP workspace folder, enabling language servers to discover
+# symbols and references across package boundaries, but these folders are not indexed by Serena,
+# i.e. the respective symbols will not be found using Serena's symbol search tools.
+# Example:
+#   additional_workspace_folders:
+#     - ../sibling-package
+#     - ../shared-lib
+ls_additional_workspace_folders: []
+
+# list of language servers to start when using the LSP backend; choose from:
+#   ada                    al                     angular                ansible                bash
+#   bsl                    clojure                cpp                    cpp_ccls               crystal
+#   csharp                 csharp_omnisharp       cue                    dart                   elixir
+#   elm                    erlang                 fortran                fsharp                 gdscript
+#   go                     groovy                 haskell                haxe                   hlsl
+#   html                   java                   json                   julia                  kotlin
+#   latex                  lean4                  lua                    luau                   markdown
+#   matlab                 msl                    nextflow               nix                    ocaml
+#   pascal                 perl                   php                    php_phpactor           php_phpantom
+#   powershell             python                 python_basedpyright    python_jedi            python_pyrefly
+#   python_ty              qml                    r                      rego                   ruby
+#   ruby_solargraph        rust                   scala                  scss                   solidity
+#   svelte                 swift                  systemverilog          terraform              toml
+#   typescript             typescript_vts         vue                    yaml                   zig
+#   (This list may be outdated; generated with scripts/print_language_list.py;
+#   For the current list, see values of the LanguageServerId enum here:
+#   https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py)
+# For some languages, there are several alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.)
+# Note:
+#   - For C, use cpp
+#   - For JavaScript, use typescript
+#   - For Angular projects, use angular (subsumes typescript+html; requires `npm install` in the project root)
+#   - For Svelte projects, use svelte (subsumes typescript/javascript for .svelte projects; requires npm)
+#   - For SCSS / Sass / plain CSS, use scss (some-sass-language-server handles all three)
+#   - For Free Pascal/Lazarus, use pascal
+# Special requirements:
+#   Some language servers require additional setup/installations.
+#   See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers
+# When using multiple language servers, the first language server that supports a given file will be used for that file.
+# The first language server is the default language and the respective language server will be used as a fallback.
+# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored.
+language_servers:
+- typescript
+- python
+
+# list of workspace folder paths (LSP backend only).
+# These folders will be used to build up Serena's symbol index.
+# Paths must be within the project root and should thus be relative to the project root.
+# Furthermore, the paths should not be filtered by ignore settings.
+# Default setting: The entire project root folder (".") is considered.
+# In (large) monorepos, this can be used to index only subfolders of the project root, e.g.
+#   ls_workspace_folders:
+#     - "./subproject1"
+#     - "./subproject2"
+ls_workspace_folders:
+- .
+
+# optional shell command to run before the language backend (LSP or JetBrains) is initialised.
+# the command runs in the project root directory and is only executed if the project is trusted
+# (see trusted_project_path_patterns in the global configuration).
+# serena waits for the command to exit: a non-zero exit code is logged as an error but does not
+# abort activation. a per-project timeout (activation_command_timeout, default 180s) is the safety
+# backstop for non-terminating commands; on expiry the process is killed and activation continues.
+# example: activation_command: "npx nx run-many -t build"
+activation_command:
+
+# maximum time in seconds to wait for activation_command to complete before killing it (default 180s).
+# must be a positive number.
+activation_command_timeout: 180.0

AGENTS.md

@@ -80,6 +80,6 @@ Stateless FastAPI — the frontend holds all scene state; the server validates i
 - **Within frontend**: components emit/subscribe on the `EventBus` and read/write the `store`; the render loop reacts to `ctx` flags (`renderInterLayerEdgesFlag`, label flags, etc.).
 
 ### Network Data Model
-- Networks upload as TSV with mandatory columns `SourceNode`, `SourceLayer`, `TargetNode`, `TargetLayer` (optional: `Weight`, `Channel`, edge color columns).
+- Networks upload as TSV with mandatory columns `SourceNode`, `SourceLayer`, `TargetNode`, `TargetLayer` (optional: `Weight`, `Channel`, edge color columns). A minimal 2-column edgelist (`SourceNode`, `TargetNode`) is also accepted — all nodes land in a single default layer.
 - Node/edge attribute files add per-node color/size/url/description and per-edge (optionally per-channel) color.
 - Sessions export/import as JSON with full node/edge/layer/scene state. `POST /api/external` returns a token URL so another app can hand off a session.

CHANGELOG.md

@@ -1,5 +1,44 @@
 # Changelog
 
+## [3.1.0] - 2026-08-10
+
+### Added
+
+- Network upload accepts a minimal 2-column edgelist (`SourceNode`, `TargetNode` only) — all nodes are spread out in a single default layer named `Layer1`. The optional `Weight` and `Channel` columns still apply. A downloadable example lives in the Help → Examples tab.
+
+- Edge weight can now be shown as **edge thickness**, not only opacity. The Edge Actions panel replaces the "Edge Opacity By Weight" checkbox with a "Show Edge Weight As" radio — Nothing / Opacity / Width / Both — plus intra- and inter-layer width sliders for whichever property weight isn't driving. Sessions carry the choice as the independent `edgeOpacityByWeight` and `edgeWidthByWeight` booleans; files written before this default to opacity, so they render unchanged. Thickness needed `Line2` (instanced quads) because WebGL renders every line primitive at exactly 1px regardless of `linewidth`.
+
+### Changed
+
+- Channel curvature sliders reach much further — intra-layer 10–60 (was 10–20), inter-layer 1–30 (was 1–10) — so the channels of a multi-channel edge can be pulled well apart instead of running nearly parallel. Defaults are unchanged, so existing sessions render exactly as before.
+
+### Fixed
+
+- Edges no longer glow. Thick edges cover a large share of the screen, and bloom on all of them was blinding against dark backgrounds. Bloom is now selective (three's off-screen bloom-composer pattern) and reads from node spheres alone, so nodes still glow, edges and layer planes stay crisp, and the extra pass costs a few spheres rather than a second full scene.
+- Curved channel edges rendered as dotted lines with beads at the curve points once thickness landed. `LineMaterial`'s `worldUnits` mode assumes a perspective camera — its fragment shader traces a view ray from the camera origin and discards anything farther than half a width from the segment, which under this app's orthographic camera discards along the whole segment. Widths are now screen-space, sized against a shared resolution uniform kept on the frustum size (so the numbers still mean world units), retargeted on resize and for the PNG export.
+- Node colors rendered washed out/dark in the 3D scene compared to the 2D navigator. The bloom composer was blitting linear color straight to the sRGB canvas (missing `OutputPass`), and the ambient light was left at the pre-r155 intensity that physical lighting divides by PI.
+
+### `Dependencies`
+
+| Tool              | Previous version | New version  |
+| ----------------- | ---------------- | ------------ |
+| fastapi           | 0.139.0          | 0.141.1      |
+| pandas            | 3.0.3            | 3.0.5        |
+| uvicorn           | 0.50.0           | 0.52.1       |
+| httpx2            | 2.5.0            | 2.10.0       |
+| mypy              | 2.1.0            | 2.3.0        |
+| pandas-stubs      | 3.0.3.260530     | 3.0.5.260730 |
+| ruff              | 0.15.20          | 0.16.2       |
+| @playwright/test  | 1.61.1           | 1.62.1       |
+| @types/three      | 0.185.0          | 0.185.4      |
+| eslint            | 10.6.0           | 10.8.1       |
+| prettier          | 3.9.4            | 3.9.6        |
+| typescript-eslint | 8.62.1           | 8.66.0       |
+| vite              | 8.1.3            | 8.2.1        |
+| vitest            | 4.1.9            | 4.1.10       |
+
+Backend dependencies updated to latest via `uv lock --upgrade`; transitives moved with them (notably starlette 1.3.1 → 1.6.0 and websockets 16.0 → 17.0.1). No known vulnerabilities on either side. `pydantic-core` stays at 2.46.4 — pydantic pins it exactly. TypeScript stays on 6.0.3: 7.0.2 typechecks fine but typescript-eslint 8.x refuses to load against the TS 7 API, so linting breaks; revisit once typescript-eslint ships TS >=7.1 support. CI now runs `uv sync --frozen` so it installs exactly the locked set the Docker image ships.
+
 ## [3.0.0] - 2026-07-27
 
 Full rewrite: migrated from R/Shiny to a **FastAPI (Python) backend + Vite / TypeScript / Three.js frontend**. Algorithms (layouts, clustering, topology) ported 1:1 via python-igraph.

README.md

@@ -1,6 +1,6 @@
 <!-- Badges -->
 
-[![Docker Pulls](https://img.shields.io/docker/pulls/pavlopouloslab/arena3dweb.svg)](https://hub.docker.com/r/pavlopouloslab/arena3d)
+[![Docker Pulls](https://img.shields.io/docker/pulls/pavlopouloslab/arena3dweb.svg)](https://hub.docker.com/r/pavlopouloslab/arena3dweb)
 [![Live Demo](https://img.shields.io/badge/demo-online-brightgreen)](https://www.arena3d.org)
 [![GitHub Repo](https://img.shields.io/badge/GitHub-PavlopoulosLab%2FArena3D-blue)](https://github.com/pavlopoulos-lab/arena3d)
 

backend/app/config.py

@@ -8,6 +8,8 @@
 # Input validation
 MANDATORY_NETWORK_COLUMNS = ["SourceNode", "SourceLayer", "TargetNode", "TargetLayer"]
 OPTIONAL_NETWORK_COLUMNS = ["Channel", "Weight"]
+# Layer assigned to every node when a minimal 2-column edgelist omits the layer columns
+DEFAULT_LAYER_NAME = "Layer1"
 MANDATORY_JSON_OBJECTS = ["layers", "nodes", "edges"]
 OPTIONAL_JSON_OBJECTS = ["scene", "universalLabelColor", "direction", "edgeOpacityByWeight"]
 MANDATORY_JSON_NODE_COLUMNS = ["name", "layer"]

backend/app/models/session.py

@@ -16,6 +16,7 @@ class SessionImportResponse(BaseModel):
     universalLabelColor: str
     direction: bool
     edgeOpacityByWeight: bool
+    edgeWidthByWeight: bool
     scramble_nodes: bool
     warnings: list[str] = []
 

backend/app/routers/network.py

@@ -11,6 +11,8 @@
 
 @router.post("/api/network", response_model=NetworkModel)
 async def upload_network(file: UploadFile) -> NetworkModel:
+    """Parse an uploaded network TSV — the 4-column Arena3D format, or a minimal
+    2-column edgelist (SourceNode, TargetNode) whose nodes all land in one default layer."""
     raw_bytes = await file.read()
     # DoS fix: reject oversized uploads before pandas parses the whole file
     # into memory — MAX_EDGES was only checked *after* the parse completed.

backend/app/services/parser.py

@@ -34,7 +34,8 @@ def _validate(df: pd.DataFrame) -> None:
     if not set(config.MANDATORY_NETWORK_COLUMNS).issubset(df.columns):
         raise NetworkValidationError(
             "Your network file must contain at least these four columns: "
-            "SourceNode, SourceLayer, TargetNode, TargetLayer"
+            "SourceNode, SourceLayer, TargetNode, TargetLayer — or just "
+            "SourceNode and TargetNode for a minimal edgelist (single layer)."
         )
     # Reject rows with an empty/whitespace mandatory cell — a blank becomes NaN
     # and would crash EdgeModel construction with a 500 instead of a clean 400.
@@ -63,6 +64,12 @@ def parse_network_tsv(text: str) -> NetworkModel:
         df = pd.read_csv(StringIO(text), sep="\t", dtype=str)
     except pd.errors.EmptyDataError as e:
         raise NetworkValidationError("The network file is empty or has no columns.") from e
+
+    # minimal 2-column edgelist: no layer columns -> every node in one default layer
+    if "SourceLayer" not in df.columns and "TargetLayer" not in df.columns:
+        df["SourceLayer"] = config.DEFAULT_LAYER_NAME
+        df["TargetLayer"] = config.DEFAULT_LAYER_NAME
+
     _validate(df)
 
     # subset legit columns (mandatory + optional Channel/Weight, in fixed order)

backend/app/services/session.py

@@ -168,6 +168,9 @@ def normalize_session(data: dict[str, Any]) -> dict[str, Any]:
         "universalLabelColor": _default(data.get("universalLabelColor"), "#FFFFFF"),
         "direction": _default(data.get("direction"), False),
         "edgeOpacityByWeight": _default(data.get("edgeOpacityByWeight"), True),
+        # Sessions written before edge thickness existed default to off, so
+        # they keep rendering exactly as they did.
+        "edgeWidthByWeight": _default(data.get("edgeWidthByWeight"), False),
         "scramble_nodes": scramble,
         "warnings": warnings,
     }

backend/tests/test_network.py

@@ -55,6 +55,24 @@ def test_missing_mandatory_column_400() -> None:
     assert "four columns" in resp.json()["detail"]
 
 
+def test_two_column_edgelist_single_default_layer() -> None:
+    body = _post("SourceNode\tTargetNode\nA\tB\nB\tC\n").json()
+    assert body["layers"] == ["Layer1"]
+    assert {n["layer"] for n in body["nodes"]} == {"Layer1"}
+    assert len(body["edges"]) == 2
+
+
+def test_two_column_edgelist_with_optional_columns() -> None:
+    body = _post("SourceNode\tTargetNode\tWeight\tChannel\nA\tB\t2\tch1\nB\tC\t4\tch2\n").json()
+    assert body["layers"] == ["Layer1"]
+    assert body["channels"] == ["ch1", "ch2"]
+
+
+def test_single_layer_column_still_400() -> None:
+    resp = _post("SourceNode\tTargetNode\tTargetLayer\nA\tB\tL1\n")
+    assert resp.status_code == 400
+
+
 def test_non_numeric_weight_400() -> None:
     tsv = f"{HDR}\tWeight\nA\tL1\tB\tL2\theavy\n"
     assert _post(tsv).status_code == 400