v1.3.0 update docs

HISTORY.md

@@ -1,6 +1,19 @@
 # History
 
-1.2.4 (2026-04-24)
+1.3.0 (2026-07-02)
+------------------
+* Adds multi-GPU support - use `--gpus` (e.g. `--gpus 0,2`) to specify which CUDA device indices `phold` and Foldseek-GPU should use. Defaults to all visible CUDA GPUs. Has no effect on MPS/XPU systems
+* Adds Intel XPU (Arc/Data Center GPU Max) support for ProstT5 prediction - thanks @linsalrob. See the [installation documentation](https://phold.readthedocs.io/en/latest/install/) for details
+* Internal migration of `phold`'s analytical/IO code from `pandas` to `polars`, improving performance especially for large datasets
+* Numerous internal performance improvements (faster masking, Foldseek database creation, sub-database and per-contig function count output writing, and faster `phold` startup via streamlined imports)
+* Fixes bugs where NCBI GenBank input containing a pseudogene CDS (no translation) or a CDS with no product would cause `phold run`/`compare` to crash #132
+* Fixes `phold plot` bug affecting genomes with CRISPR repeats and tmRNA features
+* `--restart` is more robust to interruption (fixes potential intermediate OOM issues and ensures the ProstT5 3Di prediction loop can safely resume)
+* Fixes intermittent `phold install` database download issues (adds a timeout, fixes handling of incomplete downloads, fixes database move on some filesystems)
+* Adds defensiveness around external tool (Foldseek) failures with clearer error messages
+* Adds a golden-output regression test suite so future code changes are automatically checked in CI against reference annotation outputs
+
+1.2.5 (2026-04-24)
 ------------------
 * Support `mps` (MacOS) with `phold autotune`
 
@@ -124,4 +137,4 @@ Breaking CLI parameter changes
 0.1.0 (2024-03-05)
 ------------------
 
-* Initial beta release
+* Initial beta release

README.md

@@ -122,6 +122,10 @@ conda install -c conda-forge -c bioconda phold
 
 If you are have a different non-NVIDIA GPU, or have trouble with `pytorch`, see [this link](https://pytorch.org) for more instructions. If you have an older version of CUDA installed, then you might find [this link useful](https://pytorch.org/get-started/previous-versions/).
 
+If you have an Intel machine with an XPU, see the separate [Intel XPU installation instructions](https://phold.readthedocs.io/en/latest/install/#intel-xpu).
+
+If you have multiple NVIDIA GPUs available, you can specify which to use with `--gpus` (e.g. `--gpus 0,2`) with `phold run`, `predict`, `proteins-predict` and `--foldseek_gpu` compatible commands. By default, all visible CUDA GPUs will be used.
+
 Once `phold` is installed, to download and install the database run:
 
 ```bash

docs/run.md

@@ -26,6 +26,8 @@ For `phold proteins-predict` and `phold proteins-compare`, the input will be a F
 
 `predict` uses the [ProstT5](https://github.com/mheinzinger/ProstT5) protein language model to translate protein amino acid sequences to the 3Di token alphabet used by [foldseek](https://github.com/steineggerlab/foldseek). This module is greatly accelerated if you have a GPU available and is recommended.
 
+If you have multiple NVIDIA GPUs, you can restrict which are used for ProstT5 with `--gpus` (e.g. `--gpus 0,2`). By default all visible CUDA GPUs are used. This has no effect on MPS (Apple Silicon) or Intel XPU systems.
+
 ```bash
 Usage: phold predict [OPTIONS]
 
@@ -48,6 +50,10 @@ Options:
                                  autotuning will add rather than save runtime.
   --batch_size INTEGER           batch size for ProstT5.  [default: 1]
   --cpu                          Use cpus only.
+  --gpus TEXT                    Comma-separated CUDA device indices to use
+                                 (e.g. "0,2"). Default: all visible CUDA GPUs.
+                                 Overridden by --cpu. Has no effect on MPS /
+                                 XPU systems.
   --omit_probs                   Do not output per residue 3Di probabilities
                                  from ProstT5. Mean per protein 3Di
                                  probabilities will always be output.
@@ -81,6 +87,8 @@ Alternatively, if you have provided pre-generated .pdb format protein structures
 
 `phold compare` does not use a GPU by default. However, if you have one available, you can utilise Foldseek-GPU acceleration using `--foldseek_gpu`. Note that you need to make sure your also run `phold install` with `--foldseek_gpu` prior. Regardless of whether you use `--foldseek_gpu` or not, it is recommended to use as many CPU threads with `-t` as you can (as the GPU only accelerates Foldseek's prefilter, not the alignment step).
 
+If you have multiple NVIDIA GPUs, you can restrict which are used for Foldseek-GPU with `--gpus` (e.g. `--gpus 0,2`). By default all visible CUDA GPUs are used.
+
 Example usage of `phold compare` following `phold predict`
 
 ```bash
@@ -127,6 +135,10 @@ Options:
                                 found in the input GenBank file. Helpful if
                                 you have a directory with lots of .pdb files
                                 and want to annotate only e.g. 1 phage.
+  --gpus TEXT                   Comma-separated CUDA device indices for
+                                Foldseek-GPU (e.g. "0,2"). Default: all
+                                visible CUDA GPUs. Only meaningful with
+                                --foldseek_gpu.
   -o, --output PATH             Output directory   [default: output_phold]
   -t, --threads INTEGER         Number of threads  [default: 1]
   -p, --prefix TEXT             Prefix for output files  [default: phold]
@@ -191,6 +203,10 @@ Options:
                                  autotuning will add rather than save runtime.
   --batch_size INTEGER           batch size for ProstT5.  [default: 1]
   --cpu                          Use cpus only.
+  --gpus TEXT                    Comma-separated CUDA device indices to use
+                                 (e.g. "0,2"). Default: all visible CUDA GPUs.
+                                 Overridden by --cpu. Has no effect on MPS /
+                                 XPU systems.
   --omit_probs                   Do not output per residue 3Di probabilities
                                  from ProstT5. Mean per protein 3Di
                                  probabilities will always be output.
@@ -265,6 +281,10 @@ Options:
                                  autotuning will add rather than save runtime.
   --batch_size INTEGER           batch size for ProstT5.  [default: 1]
   --cpu                          Use cpus only.
+  --gpus TEXT                    Comma-separated CUDA device indices to use
+                                 (e.g. "0,2"). Default: all visible CUDA GPUs.
+                                 Overridden by --cpu. Has no effect on MPS /
+                                 XPU systems.
   --omit_probs                   Do not output per residue 3Di probabilities
                                  from ProstT5. Mean per protein 3Di
                                  probabilities will always be output.
@@ -318,6 +338,10 @@ Options:
                                 found in the input GenBank file. Helpful if
                                 you have a directory with lots of .pdb files
                                 and want to annotate only e.g. 1 phage.
+  --gpus TEXT                   Comma-separated CUDA device indices for
+                                Foldseek-GPU (e.g. "0,2"). Default: all
+                                visible CUDA GPUs. Only meaningful with
+                                --foldseek_gpu.
   -o, --output PATH             Output directory   [default: output_phold]
   -t, --threads INTEGER         Number of threads  [default: 1]
   -p, --prefix TEXT             Prefix for output files  [default: phold]
@@ -518,6 +542,9 @@ Options:
                          want to use the default sample of 5000 Phold DB
                          proteins
   --cpu                  Use cpus only.
+  --gpus TEXT            Comma-separated CUDA device indices (e.g. "0,2").
+                         Default: lowest visible CUDA GPU. Overridden by
+                         --cpu.
   -t, --threads INTEGER  Number of threads  [default: 1]
   -d, --database TEXT    Specific path to installed phold database
   --min_batch INTEGER    Minimum batch size to test  [default: 1]

mkdocs.yml

@@ -16,6 +16,7 @@ nav:
       - Citation: citation.md
     - RUNNING:
       - Install: install.md
+      - Install (Intel XPU): install_intel_xpu.md
       - Usage: run.md
       - Output: output.md
     - TUTORIAL: