phasepred 1.0.1__tar.gz → 1.0.2__tar.gz

{phasepred-1.0.1 → phasepred-1.0.2}/CHANGELOG.md

@@ -1,5 +1,19 @@
 # Changelog
 
+## [1.0.2] - 2026-09-28
+
+Patch release for the 1.0.1 installation feedback. Model artifacts and
+training data are unchanged.
+
+### Fixed
+
+- Use `python3` in the Ubuntu venv examples.
+- Document DeepCoil's user-data installation path and show it in missing-tool
+  guidance; keep the legacy checkout environment as a fallback.
+- Show the PScore install command when `check-tools` reports it missing.
+- Let the checkout PScore runner find DBS in the installed user-data copy and
+  accept relative FASTA and output paths when invoked on its own.
+
 ## [1.0.1] - 2026-09-28
 
 Patch release based on installation and prediction feedback. Model artifacts

{phasepred-1.0.1 → phasepred-1.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phasepred
-Version: 1.0.1
+Version: 1.0.2
 Summary: Paper-faithful re-implementation of the PhaSePred phase-separation predictor (Chen et al. 2022, PNAS).
 Author: Tingting Li Lab, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University
 License-Expression: MIT

{phasepred-1.0.1 → phasepred-1.0.2}/README.md

@@ -52,7 +52,7 @@ pixi install
 ```bash
 uv venv --python 3.12 && uv pip install .
 conda env create -f environment.yml && conda activate phasepred
-python -m venv .venv && .venv/bin/pip install -e . -e packages/catgranule
+python3 -m venv .venv && .venv/bin/pip install -e . -e packages/catgranule
 ```
 
 Then install the external feature tools. Each installer is idempotent and puts

{phasepred-1.0.1 → phasepred-1.0.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phasepred"
-version = "1.0.1"
+version = "1.0.2"
 description = "Paper-faithful re-implementation of the PhaSePred phase-separation predictor (Chen et al. 2022, PNAS)."
 readme = { file = "README-pypi.md", content-type = "text/markdown" }
 license = "MIT"

{phasepred-1.0.1 → phasepred-1.0.2}/src/phasepred/__init__.py

@@ -1,3 +1,3 @@
 """PhaSePred reconstruction package."""
 
-__version__ = "1.0.1"
+__version__ = "1.0.2"

{phasepred-1.0.1 → phasepred-1.0.2}/src/phasepred/data/tools/DeepCoil/README.md

@@ -27,8 +27,10 @@ tools/DeepCoil/
 └── README.md      this file
 ```
 
-No entity is vendored — the tool lives in an isolated Python 3.8 conda env
-at `.external_envs/deepcoil` (gitignored).
+No entity is vendored — the tool lives in an isolated Python 3.8 conda env.
+New installations use `~/.local/share/phasepred/envs/deepcoil` by default,
+or `$XDG_DATA_HOME/phasepred/envs/deepcoil` / `$PHASEPRED_DATA_ROOT/envs/deepcoil`
+when set. Existing `.external_envs/deepcoil` environments remain supported.
 
 ## Install
 
@@ -38,14 +40,12 @@ bash tools/DeepCoil/install.sh --check  # verify env/bin/deepcoil present
 ```
 
 Overrides: `DEEPCOIL_ENV_PREFIX=/path/to/env DEEPCOIL_PYTHON_VERSION=3.8
-DEEPCOIL_VERSION=2.0.2`. The env prefix declared in
-`manifest.toml` `[runtime]` is `.external_envs/deepcoil`; the manifest
-`env_prefix` and the wrapper's `DEEPCOIL_ENV_PREFIX` override agree.
+DEEPCOIL_VERSION=2.0.2`. The `manifest.toml` `[runtime]` prefix names the
+legacy checkout fallback; the installer and runner prefer the user data root.
 
 ## Usage
 
 ```bash
-DEEPCOIL_ENV_PREFIX="$PWD/.external_envs/deepcoil" \
 tools/DeepCoil/run -i in.fasta -out_path /tmp/dc_out -n_cpu 4
 tools/DeepCoil/run --check
 ```
@@ -58,4 +58,4 @@ DeepCoil sanitizes output filenames (alnum + `_`). Writes
 ## Attribution
 
 Reference the DeepCoil meta-server page / Ludwiczak et al. (2019) when
-publishing scores produced by this tool.
+publishing scores produced by this tool.

{phasepred-1.0.1 → phasepred-1.0.2}/src/phasepred/data/tools/DeepCoil/manifest.toml

@@ -15,4 +15,4 @@ description = "Writes per-accession '<safe_id>.out' tab-separated files (aa, cc,
 
 [install]
 command = "bash tools/DeepCoil/install.sh"
-hint = "DeepCoil has no upstream license (not redistributable). Build the isolated Python 3.8 conda env with deepcoil==2.0.2: bash tools/DeepCoil/install.sh (env at .external_envs/deepcoil; override with DEEPCOIL_ENV_PREFIX)."
+hint = "DeepCoil has no upstream license (not redistributable). Install the isolated Python 3.8 env with deepcoil==2.0.2: bash tools/DeepCoil/install.sh (default: ~/.local/share/phasepred/envs/deepcoil; override with DEEPCOIL_ENV_PREFIX)."

{phasepred-1.0.1 → phasepred-1.0.2}/src/phasepred/data/tools/PScore/README.md

@@ -43,8 +43,9 @@ bash tools/PScore/install.sh --check  # verify predictor + DBS present
 
 ## Usage
 
-Run from anywhere; the wrapper `cd`s into `SourceCodeS2/` because the
-predictor reads `DBS/` relative to its own location:
+Run from anywhere with relative or absolute FASTA and output paths. The wrapper
+uses the installed user-data `SourceCodeS2/DBS/` when the checkout has no DBS,
+then changes into `SourceCodeS2/` as required by the predictor:
 
 ```bash
 tools/PScore/run input.fasta -output pscore.tsv -overwrite -mute
@@ -62,4 +63,4 @@ Standard output: one `PScore:  <value>  >ACC` line per scored accession
 
 Carry the reference above and the CC-BY 4.0 notice. The archived
 `SourceCodeS2/README.txt` documents the original authors. Data derived from
-the upstream `DBS/` must be attributed to Vernon et al. (2018).
+the upstream `DBS/` must be attributed to Vernon et al. (2018).

{phasepred-1.0.1 → phasepred-1.0.2}/src/phasepred/data/tools/PScore/manifest.toml

@@ -28,4 +28,4 @@ description = "One 'PScore:  <value>  >ACC' line per scored accession (via stdou
 
 [install]
 command = "bash tools/PScore/install.sh"
-hint = "PScore code is vendored (CC-BY 4.0, eLife 31486). Data (DBS) is gitignored: bash tools/PScore/install.sh --check verifies script + DBS."
+hint = "PScore is unavailable. Install its code and DBS with: bash tools/PScore/install.sh (then verify: bash tools/PScore/install.sh --check)."

{phasepred-1.0.1 → phasepred-1.0.2}/src/phasepred/data/tools/PScore/run

@@ -12,6 +12,27 @@ pkg_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 src_dir="$pkg_dir/SourceCodeS2"
 script="$src_dir/elife_phase_separation_predictor.py"
 
+# The installer writes DBS into the user data root, not the checkout. A
+# checkout runner can use that complete installation when its local DBS is
+# absent. An installed runner continues to use its adjacent SourceCodeS2.
+if [[ ! -d "$src_dir/DBS" ]]; then
+  data_root=""
+  if [[ -n "${PHASEPRED_DATA_ROOT:-}" ]]; then
+    data_root="$PHASEPRED_DATA_ROOT"
+  elif [[ -n "${XDG_DATA_HOME:-}" ]]; then
+    data_root="$XDG_DATA_HOME/phasepred"
+  elif [[ -n "${HOME:-}" ]]; then
+    data_root="$HOME/.local/share/phasepred"
+  fi
+  if [[ -n "$data_root" ]]; then
+    installed_src="$data_root/pscore/SourceCodeS2"
+    if [[ -f "$installed_src/elife_phase_separation_predictor.py" && -d "$installed_src/DBS" ]]; then
+      src_dir="$(cd "$installed_src" && pwd -P)"
+      script="$src_dir/elife_phase_separation_predictor.py"
+    fi
+  fi
+fi
+
 if [[ "${1:-}" == "--check" ]]; then
   if [[ ! -f "$script" ]]; then
     echo "PScore predictor script missing: $script" >&2
@@ -38,6 +59,10 @@ if [[ ! -f "$script" ]]; then
   echo "PScore predictor script missing: $script" >&2
   exit 1
 fi
+if [[ ! -d "$src_dir/DBS" ]]; then
+  echo "PScore DBS data missing: $src_dir/DBS (gitignored). Install with: bash $pkg_dir/install.sh" >&2
+  exit 1
+fi
 
 python_cmd=""
 for cand in "${PHASEPRED_PYTHON:-}" python3 python; do
@@ -52,5 +77,17 @@ if [[ -z "$python_cmd" ]]; then
   exit 1
 fi
 
+# The predictor must run from SourceCodeS2 so its relative DBS path works.
+# Resolve the caller's relative FASTA and -output paths before changing cwd.
+args=("$@")
+if [[ "${args[0]}" != /* ]]; then
+  args[0]="$PWD/${args[0]}"
+fi
+for ((i = 1; i < ${#args[@]} - 1; i++)); do
+  if [[ "${args[i]}" == "-output" && "${args[i+1]}" != /* ]]; then
+    args[i+1]="$PWD/${args[i+1]}"
+  fi
+done
+
 cd "$src_dir"
-exec "$python_cmd" "$script" "$@"
+exec "$python_cmd" "$script" "${args[@]}"

{phasepred-1.0.1 → phasepred-1.0.2}/src/phasepred.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phasepred
-Version: 1.0.1
+Version: 1.0.2
 Summary: Paper-faithful re-implementation of the PhaSePred phase-separation predictor (Chen et al. 2022, PNAS).
 Author: Tingting Li Lab, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University
 License-Expression: MIT

{phasepred-1.0.1 → phasepred-1.0.2}/tests/test_check_tools_table.py

@@ -22,7 +22,10 @@ from phasepred.tool_paths import ToolStatus, format_status_table
 
 pytestmark = pytest.mark.toolfree
 
-TOOLS_HINT = "Data (DBS) is gitignored: bash tools/PScore/install.sh --check verifies script + DBS."
+TOOLS_HINT = (
+    "PScore is unavailable. Install its code and DBS with: bash tools/PScore/install.sh "
+    "(then verify: bash tools/PScore/install.sh --check)."
+)
 PACKAGE_HINT = "Bundled with the phasepred wheel (deepphase_scores.tsv)."
 
 
@@ -57,6 +60,7 @@ def test_table_prints_install_hint_for_missing_rows_only() -> None:
 
     assert "Install hints:" in table
     assert "PScore: " + TOOLS_HINT in table
+    assert "bash tools/PScore/install.sh" in table
     # Reverse proof: an OK row's hint is not a remedy and must not be printed;
     # if the renderer dumped every hint (or the whole ToolStatus repr) this fails.
     assert "Build the vendored SEG binary." not in table
@@ -107,4 +111,4 @@ def test_table_has_no_hint_block_when_every_row_is_ok() -> None:
     table = format_status_table([_ok("Build the vendored SEG binary.")])
 
     assert "Install hints:" not in table
-    assert "ships only in the GitHub repository" not in table
+    assert "ships only in the GitHub repository" not in table

{phasepred-1.0.1 → phasepred-1.0.2}/tests/test_tool_contract_drift.py

@@ -21,9 +21,11 @@ from __future__ import annotations
 
 import hashlib
 import importlib
+import json
 import os
 import shutil
 import subprocess
+import sys
 import tomllib
 from pathlib import Path
 
@@ -184,3 +186,50 @@ def test_pscore_install_check_uses_installed_data_root(tmp_path: Path) -> None:
     assert result.returncode == 0, result.stdout + result.stderr
     assert f"PScore: ok ({target})" in result.stdout
     assert "DBS data missing" not in result.stderr
+
+
+def test_checkout_pscore_run_uses_installed_dbs_and_caller_paths(tmp_path: Path) -> None:
+    pkg = tmp_path / "PScore"
+    pkg.mkdir()
+    shutil.copy2(TOOLS_ROOT / "PScore" / "run", pkg / "run")
+
+    root = tmp_path / "user-data"
+    source = root / "pscore" / "SourceCodeS2"
+    (source / "DBS").mkdir(parents=True)
+    (source / "elife_phase_separation_predictor.py").write_text(
+        "import json, os, sys\n"
+        "print(json.dumps({'cwd': os.getcwd(), 'args': sys.argv[1:], "
+        "'dbs': os.path.isdir('DBS')}))\n",
+        encoding="utf-8",
+    )
+    input_file = tmp_path / "input.fasta"
+    input_file.write_text(">test\nACDEFGHIKLMNPQRSTVWY\n", encoding="utf-8")
+
+    env = os.environ.copy()
+    env["PHASEPRED_DATA_ROOT"] = str(root)
+    env["PHASEPRED_PYTHON"] = sys.executable
+    check = subprocess.run(
+        [str(pkg / "run"), "--check"],
+        cwd=tmp_path, capture_output=True, text=True, timeout=60, env=env,
+    )
+    assert check.returncode == 0, check.stderr
+
+    result = subprocess.run(
+        [str(pkg / "run"), "input.fasta", "-output", "output.tsv", "-mute"],
+        cwd=tmp_path, capture_output=True, text=True, timeout=60, env=env,
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    assert data == {
+        "cwd": str(source),
+        "args": [str(input_file), "-output", str(tmp_path / "output.tsv"), "-mute"],
+        "dbs": True,
+    }
+
+    env["PHASEPRED_DATA_ROOT"] = "user-data"
+    relative_root = subprocess.run(
+        [str(pkg / "run"), "input.fasta"],
+        cwd=tmp_path, capture_output=True, text=True, timeout=60, env=env,
+    )
+    assert relative_root.returncode == 0, relative_root.stderr
+    assert json.loads(relative_root.stdout)["args"] == [str(input_file)]