Align package version with dignity beta line

.github/workflows/elixir-denario-ex.yml

@@ -0,0 +1,46 @@
+name: Elixir DenarioEx CI
+
+on:
+  push:
+    paths:
+      - ".github/workflows/elixir-denario-ex.yml"
+      - "elixir/denario_ex/**"
+  pull_request:
+    paths:
+      - ".github/workflows/elixir-denario-ex.yml"
+      - "elixir/denario_ex/**"
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: elixir/denario_ex
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Erlang and Elixir
+        uses: erlef/setup-beam@v1
+        with:
+          elixir-version: "1.18.4"
+          otp-version: "28.0"
+
+      - name: Restore Mix cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.mix
+            ~/.hex
+            elixir/denario_ex/deps
+            elixir/denario_ex/_build
+          key: ${{ runner.os }}-elixir-denario-ex-${{ hashFiles('elixir/denario_ex/mix.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-elixir-denario-ex-
+
+      - name: Install dependencies
+        run: mix deps.get
+
+      - name: Run tests
+        run: mix test

.gitignore

@@ -32,6 +32,8 @@ eggs/
 .eggs/
 lib/
 lib64/
+!elixir/denario_ex/lib/
+!elixir/denario_ex/lib/**
 parts/
 sdist/
 var/
@@ -73,6 +75,7 @@ cover/
 
 # Django stuff:
 *.log
+erl_crash.dump
 local_settings.py
 db.sqlite3
 db.sqlite3-journal

README.md

@@ -84,6 +84,28 @@ Generate a research idea from that data specification.
 den.get_idea()
 ```
 
+Optionally, give Denario a short researcher statement so the paper-writing stages preserve your framing and priorities rather than defaulting only to generic scientific tone.
+
+```python
+den.set_researcher_statement(
+    "Emphasize robustness and measurement limits. Do not overclaim causality."
+)
+```
+
+If you want to compare multiple directions before converging, generate candidate branches and build a comparison template:
+
+```python
+den.generate_idea_branches(count=3)
+den.build_idea_comparison(
+    criteria=[
+        "Novelty",
+        "Feasibility with this dataset",
+        "Fit to the intended paper contribution",
+    ]
+)
+den.select_idea_candidate(2)
+```
+
 Generate the methodology required for working on that idea.
 
 ```python
@@ -96,6 +118,14 @@ With the methodology setup, perform the required computations and get the plots
 den.get_results()
 ```
 
+Before paper generation, Denario now requires explicit human sign-off that the generated artifacts were reviewed and that a human accepts authorship responsibility.
+
+```python
+den.confirm_authorship(
+    "I checked the claims against the results, reviewed the citations, and rewrote the sections I will stand behind."
+)
+```
+
 Finally, generate a latex article with the results. You can specify the journal style, in this example we choose the [APS (Physical Review Journals)](https://journals.aps.org/) style.
 
 ```python
@@ -110,6 +140,10 @@ You can also manually provide any info as a string or markdown file in an interm
 den.set_method(path_to_the_method_file.md)
 ```
 
+You can also provide a `researcher_statement.md` artifact through `set_researcher_statement(...)` if you want the paper-writing stages to preserve a particular stance, emphasis, or constraint.
+
+Similarly, `generate_idea_branches(...)`, `generate_method_branches(...)`, `build_idea_comparison(...)`, `build_method_comparison(...)`, `select_idea_candidate(...)`, and `select_method_candidate(...)` support a compare-before-converge workflow.
+
 ## DenarioApp
 
 You can run Denario using a GUI through the [DenarioApp](https://github.com/AstroPilot-AI/DenarioApp).

denario/__init__.py

@@ -1,7 +1,12 @@
+from ._compat import patch_mistralai_for_cmbagent
+
+patch_mistralai_for_cmbagent()
+
 from .denario import Denario, Research, Journal, LLM, models, KeyManager
 from .config import REPO_DIR
+from .exceptions import AuthorshipConfirmationError
 
-__all__ = ['Denario', 'Research', 'Journal', 'REPO_DIR', 'LLM', "models", "KeyManager"]
+__all__ = ['Denario', 'Research', 'Journal', 'REPO_DIR', 'LLM', "models", "KeyManager", "AuthorshipConfirmationError"]
 
 from importlib.metadata import version, PackageNotFoundError
 

denario/_compat.py

@@ -0,0 +1,35 @@
+"""Compatibility helpers for third-party dependencies."""
+
+from __future__ import annotations
+
+import importlib
+
+
+def patch_mistralai_for_cmbagent() -> None:
+    """Expose legacy top-level Mistral symbols expected by ``cmbagent``.
+
+    ``cmbagent`` imports ``Mistral`` and ``DocumentURLChunk`` from the top-level
+    ``mistralai`` module, while newer ``mistralai`` releases place them under
+    nested modules. Patch those attributes in when needed so Denario keeps
+    working across both layouts.
+    """
+
+    try:
+        mistralai = importlib.import_module("mistralai")
+    except Exception:
+        return
+
+    try:
+        if not hasattr(mistralai, "Mistral"):
+            mistral_sdk = importlib.import_module("mistralai.client.sdk")
+            mistralai.Mistral = mistral_sdk.Mistral
+
+        if not hasattr(mistralai, "DocumentURLChunk"):
+            document_module = importlib.import_module(
+                "mistralai.client.models.documenturlchunk"
+            )
+            mistralai.DocumentURLChunk = document_module.DocumentURLChunk
+    except Exception:
+        # Leave the environment unchanged if the dependency moves again;
+        # downstream imports will surface the real error in that case.
+        return

denario/config.py

@@ -18,8 +18,15 @@
 PAPER_FOLDER = "paper"
 
 DESCRIPTION_FILE = "data_description.md"
+RESEARCHER_STATEMENT_FILE = "researcher_statement.md"
 IDEA_FILE = "idea.md"
+IDEA_CANDIDATES_FILE = "idea_candidates.md"
+IDEA_COMPARISON_FILE = "idea_comparison.md"
 METHOD_FILE = "methods.md"
+METHOD_CANDIDATES_FILE = "method_candidates.md"
+METHOD_COMPARISON_FILE = "method_comparison.md"
 RESULTS_FILE = "results.md"
 LITERATURE_FILE = "literature.md"
 REFEREE_FILE = "referee.md"
+AUTHORSHIP_CONFIRMATION_FILE = "authorship_confirmation.md"
+BRANCH_WORKSPACES_DIR = "branch_workspaces"