Merge pull request #540 from padix-key/info

Save datasets in `structure.info` as BinaryCIF

.gitattributes

@@ -1,3 +1,4 @@
 tests/structure/data/* linguist-vendored
 tests/sequence/data/* linguist-vendored
 src/biotite/sequence/align/matrix_data/* linguist-vendored
+src/biotite/structure/info/ccd/components.bcif filter=lfs diff=lfs merge=lfs -text

.github/workflows/test_and_deploy.yml

@@ -37,7 +37,9 @@ jobs:
     outputs:
       include: ${{ steps.set-matrix.outputs.include }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+        with:
+          lfs: true
       - name: Install cibuildwheel
         # MAKE SURE THIS STAYS IN SYNC WITH THE LOWER GHA cibuildwheel
         run: pipx install cibuildwheel==2.16.5
@@ -72,7 +74,9 @@ jobs:
         include: ${{ fromJson(needs.generate-wheels-matrix.outputs.include) }}
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+        with:
+          lfs: true
 
       # QEMU enables building/testing for non-native architectures (ie arm64)
       # at the cost of speed
@@ -103,7 +107,9 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+        with:
+          lfs: true
       - uses: conda-incubator/setup-miniconda@v2
         with:
           environment-file: environment.yml
@@ -138,7 +144,9 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+        with:
+          lfs: true
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: biotite-dev
@@ -159,10 +167,9 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
-        fetch-depth: 0
-        submodules: true
+        lfs: true
     - name: Build source distribution
       run: pipx run build --sdist
     - uses: actions/upload-artifact@v3
@@ -182,7 +189,9 @@ jobs:
       NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+      with:
+        lfs: true
     - uses: conda-incubator/setup-miniconda@v2
       with:
         environment-file: environment.yml

doc/install.rst

@@ -8,11 +8,7 @@ Installation
 Requirements
 ------------
 
-*Biotite* requires at least *Python* version 3.6. If you are still using
-*Python* 2.7, you should `hurry up <https://pythonclock.org/>`_ with upgrading
-to *Python* 3.
-
-*Biotite* also requires the following packages:
+*Biotite* requires at least *Python* version 3.7 and the following packages:
 
    - **numpy**
    - **requests**
@@ -78,24 +74,24 @@ Note that installing from source distribution requires a C-compiler
 Install from source
 -------------------
 
-If you want to install *Biotite* from the
-`project repository <https://github.com/biotite-dev/biotite>`_, navigate to the
-top-level directory of your local *Biotite* repository clone (the one
-``setup.py`` is in) and type the following:
-
-.. code-block:: console
+You can also install Biotite from the
+`project repository <https://github.com/biotite-dev/biotite>`_.
+The repository uses `Git LFS <https://git-lfs.com/>`_ to store large binary
+files, which needs to be installed first.
 
-   $ pip install .
+.. note::
+   In case installing *Git LFS* is not an option: The binary file can also be
+   downloaded manually from
+   `here <https://github.com/biotite-dev/biotite/raw/info/src/biotite/structure/info/ccd/components.bcif>`.
+   Then the ``biotite/structure/info/ccd/components.bcif`` file in the
+   repository needs to be replaced with the downloaded file.
 
-Note that this requires a C-compiler (typically GCC) and the packages
-`cython` and `wheel` to be installed.
-For convenience
-`this Conda environment <http://raw.githubusercontent.com/biotite-dev/biotite/master/environment.yml>`_
-contains all runtime and build dependencies for *Biotite*:
+After cloning the repository, navigate to its top-level directory (the one
+``setup.py`` is in) and type the following:
 
 .. code-block:: console
 
-   conda env create -f environment.yml
+   $ pip install .
 
 Having the *Biotite* package always pointing to your directory containing the
 repository is also possible.
@@ -105,17 +101,6 @@ Type the following in the top-level directory:
 
    $ pip install -e .
 
-To generate the wheels and source distribution for upload to PyPI (most
-probably you won't need that, but just in case), simply type:
-
-.. code-block:: console
-
-   $ python setup.py bdist_wheel
-   $ python setup.py sdist
-
-You can find the created wheel and the source distribution in the ``dist``
-directory.
-
 
 Common issues and solutions
 ---------------------------

setup.py

@@ -84,7 +84,7 @@ def get_extensions():
         # Codon tables
         "biotite.sequence"          : ["codon_tables.txt"],
         # Structure data (masses, bonds, etc.)
-        "biotite.structure.info"    : ["*.json", "*.msgpack"]
+        "biotite.structure.info"    : ["atom_masses.json", "ccd/*"]
     },
 )