Add paper CLI: download academic papers by DOI and convert to markdown

Downloads PDFs from LibGen (primary) or Anna's Archive API (fallback),
converts to markdown via marker_single, and prints to stdout. Includes
XDG-compliant caching, nix flake with marker-pdf packaging, and a
Claude Code skill for paper-reader integration.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

nix/marker.nix

@@ -0,0 +1,136 @@
+# Nix expressions for marker-pdf and its missing dependencies.
+{ pkgs }:
+
+let
+  python3Packages = pkgs.python3Packages;
+
+  # pypdfium2 4.30.0 — pinned because pdftext and surya-ocr require v4.x API.
+  # Installed from the manylinux wheel which bundles libpdfium.
+  pypdfium2 = python3Packages.buildPythonPackage rec {
+    pname = "pypdfium2";
+    version = "4.30.0";
+    format = "wheel";
+
+    src = pkgs.fetchurl {
+      url = "https://files.pythonhosted.org/packages/65/cd/3f1edf20a0ef4a212a5e20a5900e64942c5a374473671ac0780eaa08ea80/pypdfium2-4.30.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
+      hash = "sha256-8feNIYng3fmsK3qbm9Twxm9U0Tif9sF+n9ncA00G6z8=";
+    };
+
+    nativeBuildInputs = [ pkgs.autoPatchelfHook ];
+    buildInputs = [ pkgs.stdenv.cc.cc.lib ];
+
+    pythonImportsCheck = [ "pypdfium2" ];
+  };
+
+  pdftext = python3Packages.buildPythonPackage rec {
+    pname = "pdftext";
+    version = "0.6.3";
+    pyproject = true;
+
+    src = pkgs.fetchPypi {
+      inherit pname version;
+      hash = "sha256-q1xd/g8ft43h24N8ytrB6kGwfOGJD+rZc8moTNr1Tew=";
+    };
+
+    build-system = [ python3Packages.poetry-core ];
+    nativeBuildInputs = [ python3Packages.pythonRelaxDepsHook ];
+    pythonRelaxDeps = true;
+
+    dependencies = [
+      pypdfium2
+      python3Packages.pydantic
+      python3Packages.pydantic-settings
+      python3Packages.click
+    ];
+
+    # Tests require PDF fixtures not included in the sdist
+    doCheck = false;
+    pythonImportsCheck = [ "pdftext" ];
+  };
+
+  surya-ocr = python3Packages.buildPythonPackage rec {
+    pname = "surya-ocr";
+    version = "0.17.1";
+    pyproject = true;
+
+    src = pkgs.fetchPypi {
+      pname = "surya_ocr";
+      inherit version;
+      hash = "sha256-NJ142FTB7V+Bblg1Re1kUaoLxpkuKDqAUDR5mqzujCQ=";
+    };
+
+    build-system = [ python3Packages.poetry-core ];
+    nativeBuildInputs = [ python3Packages.pythonRelaxDepsHook ];
+    pythonRelaxDeps = true;
+    pythonRemoveDeps = [ "pre-commit" ];
+
+    dependencies = [
+      python3Packages.transformers
+      python3Packages.torch
+      python3Packages.pydantic
+      python3Packages.pydantic-settings
+      python3Packages.python-dotenv
+      python3Packages.pillow
+      pypdfium2
+      python3Packages.filetype
+      python3Packages.click
+      python3Packages.platformdirs
+      python3Packages.opencv-python-headless
+      python3Packages.einops
+    ];
+
+    # Tests require model weights and GPU
+    doCheck = false;
+    pythonImportsCheck = [ "surya" ];
+  };
+
+  marker-pdf = python3Packages.buildPythonPackage rec {
+    pname = "marker-pdf";
+    version = "1.10.2";
+    pyproject = true;
+
+    src = pkgs.fetchPypi {
+      pname = "marker_pdf";
+      inherit version;
+      hash = "sha256-zg/IOeEa11GaV20lTKnVGg+UVLnX2gIhH3IrFBMX+fE=";
+    };
+
+    build-system = [ python3Packages.poetry-core ];
+    nativeBuildInputs = [ python3Packages.pythonRelaxDepsHook ];
+    pythonRelaxDeps = true;
+    pythonRemoveDeps = [ "pre-commit" ];
+
+    dependencies = [
+      python3Packages.pillow
+      python3Packages.pydantic
+      python3Packages.pydantic-settings
+      python3Packages.transformers
+      python3Packages.python-dotenv
+      python3Packages.torch
+      python3Packages.tqdm
+      python3Packages.ftfy
+      python3Packages.rapidfuzz
+      surya-ocr
+      python3Packages.regex
+      pdftext
+      python3Packages.markdownify
+      python3Packages.click
+      python3Packages.markdown2
+      python3Packages.filetype
+      python3Packages.google-genai
+      python3Packages.anthropic
+      python3Packages.scikit-learn
+      python3Packages.openai
+    ];
+
+    # Tests require model weights
+    doCheck = false;
+    pythonImportsCheck = [ "marker" ];
+  };
+in
+{
+  inherit pypdfium2 pdftext surya-ocr marker-pdf;
+
+  # Python environment with marker_single on PATH
+  markerEnv = python3Packages.python.withPackages (_: [ marker-pdf ]);
+}