Rename the package to blochsim and add its logo

.github/DISCUSSION_TEMPLATE/ideas.yml

@@ -5,7 +5,7 @@ body:
     attributes:
       label: The idea
       description: |
-        A model, an interface or a direction you think TorchSim should take,
+        A model, an interface or a direction you think BlochSim should take,
         before it is concrete enough to be a feature request.
     validations:
       required: true

.github/DISCUSSION_TEMPLATE/q-a.yml

@@ -20,5 +20,5 @@ body:
   - type: input
     id: version
     attributes:
-      label: TorchSim version
+      label: BlochSim version
       placeholder: "0.4.1, or the commit you are on"

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -5,8 +5,8 @@ body:
   - type: markdown
     attributes:
       value: |
-        Questions about how to use TorchSim, and results you are unsure about,
-        belong in [Discussions](https://github.com/pulserver/torchsim/discussions).
+        Questions about how to use BlochSim, and results you are unsure about,
+        belong in [Discussions](https://github.com/pulserver/blochsim/discussions).
         This form is for behaviour you can pin down.
 
   - type: textarea
@@ -47,7 +47,7 @@ body:
         Paste the output of
 
         ```sh
-        python -c "from importlib.metadata import version; print('torchsim', version('torchsim'))"
+        python -c "from importlib.metadata import version; print('blochsim', version('blochsim'))"
         python -c "import torch; print(torch.__version__, torch.version.cuda, torch.cuda.get_device_name() if torch.cuda.is_available() else 'cpu')"
         python -VV
         ```

.github/ISSUE_TEMPLATE/config.yml

@@ -1,8 +1,8 @@
 blank_issues_enabled: false
 contact_links:
   - name: Question, or a result you are unsure about
-    url: https://github.com/pulserver/torchsim/discussions
+    url: https://github.com/pulserver/blochsim/discussions
     about: Ask how to model a sequence, or whether a signal you got is expected.
   - name: Security report
-    url: https://github.com/pulserver/torchsim/security/policy
+    url: https://github.com/pulserver/blochsim/security/policy
     about: Report a vulnerability privately rather than in a public issue.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: A sequence, a physical effect, an estimator or an interface TorchSim should carry.
+description: A sequence, a physical effect, an estimator or an interface BlochSim should carry.
 labels: ["enhancement"]
 body:
   - type: textarea
@@ -16,7 +16,7 @@ body:
   - type: textarea
     id: proposal
     attributes:
-      label: What you would like TorchSim to do
+      label: What you would like BlochSim to do
       description: |
         If you already know the shape of it -- an operator, a tissue property,
         a keyword on an existing simulator -- sketch the call you would like

.github/PULL_REQUEST_TEMPLATE.md

@@ -23,6 +23,6 @@ pytest tests/
 - [ ] Comments and docstrings describe the code as it is now -- no
       "previously", no "this replaces", no naming of a bug that is fixed.
 - [ ] A change to what the kernels compute is in both of them, and arrives
-      with a test that pins it against something outside TorchSim.
+      with a test that pins it against something outside BlochSim.
 - [ ] The documentation is updated where the change is visible to a caller,
       and `bash scripts/build_docs.sh` still builds.

.github/SECURITY.md

@@ -10,7 +10,7 @@ Older releases are not patched.
 Report privately, not as a public issue:
 
 - open a draft advisory through
-  [Security -> Report a vulnerability](https://github.com/pulserver/torchsim/security/advisories/new),
+  [Security -> Report a vulnerability](https://github.com/pulserver/blochsim/security/advisories/new),
   which is the preferred route; or
 - email **matteo.cencini@gmail.com** if you cannot use GitHub.
 
@@ -22,7 +22,7 @@ publicly.
 
 ## Scope
 
-TorchSim executes the code you give it: a sequence layout, a cost function and
+BlochSim executes the code you give it: a sequence layout, a cost function and
 a signal model are all Python that runs in your process, so a malicious
 *script* is out of scope in the same way it is for NumPy or PyTorch.
 
@@ -36,4 +36,4 @@ merely a bug.
 ## Not a vulnerability
 
 A simulation that returns wrong physics, diverges, or raises is a
-[bug report](https://github.com/pulserver/torchsim/issues/new/choose).
+[bug report](https://github.com/pulserver/blochsim/issues/new/choose).

.github/skills/add-a-sequence/SKILL.md

@@ -1,9 +1,9 @@
 ---
 name: add-a-sequence
-description: Write a new simulator, signal model, or sequence operator in TorchSim. Use when asked to add a sequence, a readout module, a physical effect, or a tissue property.
+description: Write a new simulator, signal model, or sequence operator in BlochSim. Use when asked to add a sequence, a readout module, a physical effect, or a tissue property.
 ---
 
-# Add a sequence to TorchSim
+# Add a sequence to BlochSim
 
 **There is one base class, `Simulator`, written in one of two ways.** Nothing
 downstream ever asks which way.
@@ -62,15 +62,15 @@ and a run reads which properties were passed to decide which terms the kernel
 evaluates. Adding an effect is one line in a model's property declaration, plus
 the term itself in **both** kernels.
 
-The shared parameter ABI is `src/torchsim/sequence/_parameters.py`, read by the
+The shared parameter ABI is `src/blochsim/sequence/_parameters.py`, read by the
 Python dispatch, the C++ extension and the Triton kernels. A parameter added
 there is added in all three or in none.
 
 ## What the change has to arrive with
 
-A test that pins the new physics against something **outside** TorchSim: a
+A test that pins the new physics against something **outside** BlochSim: a
 closed form, a published figure, or an isochromat summation written out in the
-test itself. Comparing TorchSim to TorchSim proves the two agree, which was
+test itself. Comparing BlochSim to BlochSim proves the two agree, which was
 never in doubt. Put it in `tests/epg/` and state the invariant in the module
 docstring.
 

.github/skills/build-and-test/SKILL.md

@@ -1,9 +1,9 @@
 ---
 name: build-and-test
-description: Compile the C++ kernels and run the TorchSim suite, including the Triton paths on a machine with no GPU. Use when asked to build, install, test, or reproduce a failure in torchsim.
+description: Compile the C++ kernels and run the BlochSim suite, including the Triton paths on a machine with no GPU. Use when asked to build, install, test, or reproduce a failure in blochsim.
 ---
 
-# Build and test TorchSim
+# Build and test BlochSim
 
 ## Install
 
@@ -15,7 +15,7 @@ pip install -e ".[dev]" ; echo "exit: $?"
 run alone, `pip install -e ".[test]"` is enough and much smaller.
 
 An editable install puts the Python sources on the path, so an edit under
-`src/torchsim` takes effect on the next import. The two C++ extensions are
+`src/blochsim` takes effect on the next import. The two C++ extensions are
 compiled artifacts and do not: re-run the install after editing any `.cpp`.
 
 **Read the exit status, not the output.** A failed compile leaves the
@@ -24,7 +24,7 @@ that no longer corresponds to the source. Confirm the extension is the one you
 just built:
 
 ```sh
-python -c "import torchsim._epg_cpu as k; print(k.__file__)"
+python -c "import blochsim._epg_cpu as k; print(k.__file__)"
 ```
 
 ## Test

.github/skills/build-the-docs/SKILL.md

@@ -1,37 +1,37 @@
 ---
 name: build-the-docs
-description: Build the TorchSim documentation, add a figure to an explanation page, or add a gallery example. Use when asked about docs, Sphinx, the gallery, MyST, or Read the Docs for torchsim.
+description: Build the BlochSim documentation, add a figure to an explanation page, or add a gallery example. Use when asked about docs, Sphinx, the gallery, MyST, or Read the Docs for blochsim.
 ---
 
-# Build the TorchSim documentation
+# Build the BlochSim documentation
 
 ```sh
 bash scripts/build_docs.sh              # incremental
 bash scripts/build_docs.sh --clean      # re-execute every example
-PYTHON_BIN=~/envs/torchsim/bin/python bash scripts/build_docs.sh
+PYTHON_BIN=~/envs/blochsim/bin/python bash scripts/build_docs.sh
 python -m http.server --directory docs/build/html 8000
 ```
 
-The script checks that the interpreter it is given can import TorchSim and the
+The script checks that the interpreter it is given can import BlochSim and the
 documentation extensions, then builds into `docs/build/html`. Two things make
 it slower than a plain Sphinx run and are the point of it: **sphinx-gallery
 executes the examples**, and **the explanation pages' figures are re-rendered**
-by `docs/explanation_figures.py` with the TorchSim in your working tree.
+by `docs/explanation_figures.py` with the BlochSim in your working tree.
 
 An example is executed when the interpreter can import everything it imports:
 an environment with the `dev` or `examples` extra runs the whole gallery, one
-with `doc` alone runs what needs nothing but TorchSim. A page already carrying
+with `doc` alone runs what needs nothing but BlochSim. A page already carrying
 output executed from the source as it stands is reused rather than re-run, and
 the build names each example it did not run and where its output came from. To
 build the pages without running any of them, pass `-D plot_gallery=0`.
 
 ## Where the published pages are built
 
 `.github/workflows/docs.yml` builds them, and GitHub Pages serves them from
-the `gh-pages` branch at <https://pulserver.github.io/torchsim/>.
+the `gh-pages` branch at <https://pulserver.github.io/blochsim/>.
 
 Its **HTML** job runs on every branch and pull request with the `doc` extra:
-every page is written and the examples needing nothing but TorchSim are
+every page is written and the examples needing nothing but BlochSim are
 executed, in a few minutes, and the tree is uploaded as an artifact to read.
 
 Its **Site** job runs on `main`, on a `v*.*.*` tag and on demand. It installs
@@ -43,7 +43,7 @@ Sphinx wrote to `scripts/publish_docs.py`, which places it in the site:
     site/index.html  a page sending a reader to the newest release
     site/versions.json  the list the switcher in the sidebar reads
 
-`TORCHSIM_DOCS_VERSION` is what a build calls itself; it names the directory,
+`BLOCHSIM_DOCS_VERSION` is what a build calls itself; it names the directory,
 the switcher's mark and the Binder path prefix, and defaults to `latest`.
 
 ## Markdown, and the two places it is not
@@ -90,7 +90,7 @@ executed and where it is published as source.
 ## Writing
 
 The audience is MR scientists: pulse sequences and physics, not software
-architecture. Describe what TorchSim does and why that is right on its own
+architecture. Describe what BlochSim does and why that is right on its own
 terms. These pages are not a changelog — never justify a design by describing
 the design it replaced.
 
@@ -109,7 +109,7 @@ Keep the public sidebar shallow and in this order:
 The first four Framework examples are the Course. They teach the public
 abstraction in order; the remaining example sections are standalone Tours.
 
-For a new sequence, teach {class}`torchsim.model.Simulator` as the extension
+For a new sequence, teach {class}`blochsim.model.Simulator` as the extension
 point. A state-machine simulator has two complementary inputs: its class-level
 handlers interpret commands from an incoming Pulseq/MRD description, and
 `layout()` constructs the same sequence offline. Lower-level

.github/skills/cut-a-release/SKILL.md

@@ -1,9 +1,9 @@
 ---
 name: cut-a-release
-description: Publish a TorchSim release to PyPI, and diagnose a wheel build. Use when asked about releasing, versioning, cibuildwheel, abi3 wheels, or the packaging setup.
+description: Publish a BlochSim release to PyPI, and diagnose a wheel build. Use when asked about releasing, versioning, cibuildwheel, abi3 wheels, or the packaging setup.
 ---
 
-# Cut a TorchSim release
+# Cut a BlochSim release
 
 The version comes from the git tag through setuptools-scm; nothing in the tree
 states it. To release:

.github/workflows/docs.yml

@@ -46,7 +46,7 @@ jobs:
             --extra-index-url https://pypi.org/simple
 
       # The ``doc`` extra alone: every page is written and the examples
-      # needing nothing but TorchSim are executed, which is what a branch
+      # needing nothing but BlochSim are executed, which is what a branch
       # wants to know within a few minutes. The Site job below runs the rest.
       - name: Build the extensions and install
         run: python -m pip install ".[doc]"
@@ -86,7 +86,7 @@ jobs:
       # A tag is published under its own name; anything else is the
       # development version. It names the directory of the site, the entry
       # the switcher marks, and the prefix the notebook links reach through.
-      TORCHSIM_DOCS_VERSION: ${{ github.ref_type == 'tag' && github.ref_name || 'latest' }}
+      BLOCHSIM_DOCS_VERSION: ${{ github.ref_type == 'tag' && github.ref_name || 'latest' }}
 
     steps:
       - uses: actions/checkout@v7
@@ -125,7 +125,7 @@ jobs:
 
       - uses: actions/upload-artifact@v7
         with:
-          name: html-${{ env.TORCHSIM_DOCS_VERSION }}
+          name: html-${{ env.BLOCHSIM_DOCS_VERSION }}
           path: docs/build/html
           retention-days: 7
 
@@ -141,8 +141,8 @@ jobs:
           else
             git worktree add --orphan ../pages
           fi
-          python scripts/publish_docs.py docs/build/html "$TORCHSIM_DOCS_VERSION" ../pages
+          python scripts/publish_docs.py docs/build/html "$BLOCHSIM_DOCS_VERSION" ../pages
           git -C ../pages add --all
           git -C ../pages commit --quiet \
-            -m "Publish $TORCHSIM_DOCS_VERSION from ${{ github.sha }}" || exit 0
+            -m "Publish $BLOCHSIM_DOCS_VERSION from ${{ github.sha }}" || exit 0
           git -C ../pages push origin HEAD:gh-pages

.github/workflows/test.yml

@@ -67,7 +67,7 @@ jobs:
         shell: python
         run: |
           import importlib.util, pathlib
-          spec = importlib.util.find_spec("torchsim")
+          spec = importlib.util.find_spec("blochsim")
           root = pathlib.Path(next(iter(spec.submodule_search_locations)))
           for kernel in sorted(root.glob("_*_cpu*")):
               print(kernel.name, kernel.stat().st_size, "bytes")
@@ -84,6 +84,6 @@ jobs:
         uses: codecov/codecov-action@v7
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          slug: pulserver/torchsim
+          slug: pulserver/blochsim
           files: coverage.xml
           fail_ci_if_error: false

.github/workflows/wheels.yml

@@ -10,8 +10,8 @@ on:
       - pyproject.toml
       - CMakeLists.txt
       - setup.py
-      - "src/torchsim/*.cpp"
-      - "src/torchsim/*.hpp"
+      - "src/blochsim/*.cpp"
+      - "src/blochsim/*.hpp"
       - scripts/check_wheel.py
       - .github/workflows/wheels.yml
   workflow_dispatch:
@@ -95,7 +95,7 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/p/torchsim
+      url: https://pypi.org/p/blochsim
     permissions:
       # Trusted publishing: no API token is stored anywhere.
       id-token: write

.gitignore

@@ -21,7 +21,7 @@ CMakeFiles/
 cmake_install.cmake
 
 # Generated at build time
-src/torchsim/_version.py
+src/blochsim/_version.py
 
 # Test and coverage output
 .coverage*

.pre-commit-config.yaml

@@ -4,7 +4,7 @@
 ci:
   autoupdate_schedule: monthly
 
-exclude: ^src/torchsim/_version\.py$
+exclude: ^src/blochsim/_version\.py$
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks