Merge branch 'feature/profile-grids' of ssh://localhost:14147/Users/p…

…ett/src/chimerax into feature/profile-grids
RBVI · Dec 28, 2024 · b7b40d0 · b7b40d0
2 parents f5c8da2 + 139b296
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diff --git a/.github/workflows/flatpak_build.yml b/.github/workflows/flatpak_build.yml
@@ -39,6 +39,20 @@ jobs:
             linux-bundles.tar.gz
             linux-include.tar.gz
           key: linux-bundles-${{ inputs.release_type }}-${{ github.sha }}
+      - name: Install jq
+        run: dnf install -y jq
+      - uses: Tiryoh/gha-jobid-action@v1
+        id: get_job_id
+        with:
+          job_name: "Build ChimeraX FlatPak / flatpak-build"
+      - name: Note the run and job IDs on Plato
+        uses: ./utils/ci/nightly_logs
+        with:
+          platform: flatpak
+          deploy_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+          run_id: ${{ github.run_id }}
+          job_id: ${{ steps.get_job_id.outputs.job_id }}
+          build_type: daily
       - run: chown -R $(id -u):$(id -g) $PWD
       - name: Unpack the bundles to build/sync
         run: |

diff --git a/.github/workflows/mac_arm_build.yml b/.github/workflows/mac_arm_build.yml
@@ -42,7 +42,7 @@ jobs:
         uses: Homebrew/actions/setup-homebrew@master
       - run: |
           brew install [email protected]
-          python3.10 -m pip install lief==0.12.2 dmgbuild
+          python3.10 -m pip install lief dmgbuild
           patch --ignore-whitespace -d /opt/homebrew/lib/python3.10/site-packages/dmgbuild -N -p0 < ./utils/build/macos/dmgbuild.patch
       - uses: actions/checkout@v4
       - run: ${PWD}/utils/set_up_macos.sh
@@ -52,6 +52,18 @@ jobs:
           platform: macos
           architecture: arm64
           cache_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+      - uses: Tiryoh/gha-jobid-action@v1
+        id: get_job_id
+        with:
+          job_name: "Build ChimeraX for arm64 macOS / build-arm-macos"
+      - name: Note the run and job IDs on Plato
+        uses: ./utils/ci/nightly_logs
+        with:
+          platform: mac_arm64
+          deploy_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+          run_id: ${{ github.run_id }}
+          job_id: ${{ steps.get_job_id.outputs.job_id }}
+          build_type: daily
       - run: MAKEOPTS="-j$(sysctl -n hw.logicalcpu)" make -j$(sysctl -n hw.logicalcpu) install-rbvi
       - name: Run the legacy test suite
         run: make test

diff --git a/.github/workflows/mac_intel_build.yml b/.github/workflows/mac_intel_build.yml
@@ -28,6 +28,9 @@ on:
       MAC_NOTARIZATION_EMAIL:
         required: true
 
+env:
+  MACOSX_DEPLOYMENT_TARGET: 11
+
 jobs:
   build-intel-macos:
     name: Build ChimeraX for Intel Macs
@@ -41,7 +44,7 @@ jobs:
         uses: Homebrew/actions/setup-homebrew@master
       - run: |
           brew install [email protected]
-          python3.10 -m pip install lief==0.12.2 dmgbuild
+          python3.10 -m pip install lief dmgbuild
           patch --ignore-whitespace -d /usr/local/lib/python3.10/site-packages/dmgbuild -N -p0 < ./utils/build/macos/dmgbuild.patch
       # Temporarily force this to succeed. The container's Python conflicts with homebrew's,
       # but we don't really use it anyway.
@@ -52,6 +55,18 @@ jobs:
           platform: macos
           architecture: x86_64
           cache_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+      - uses: Tiryoh/gha-jobid-action@v1
+        id: get_job_id
+        with:
+          job_name: "Build ChimeraX for Intel macOS / Build ChimeraX for Intel Macs"
+      - name: Note the run and job IDs on Plato
+        uses: ./utils/ci/nightly_logs
+        with:
+          platform: macosx
+          deploy_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+          run_id: ${{ github.run_id }}
+          job_id: ${{ steps.get_job_id.outputs.job_id }}
+          build_type: daily
       - run: MAKEOPTS="-j$(sysctl -n hw.logicalcpu)" make -j$(sysctl -n hw.logicalcpu) install-rbvi
       - name: Run the legacy test suite
         run: make test

diff --git a/.github/workflows/mac_universal_build.yml b/.github/workflows/mac_universal_build.yml
@@ -39,10 +39,22 @@ jobs:
         run: |
           brew install [email protected]
           python3.10 -m pip install setuptools==54.0
-          python3.10 -m pip install lief==0.12.2
+          python3.10 -m pip install lief
           python3.10 -m pip install dmgbuild
           # Make dmgbuild allocate an adult sized DMG
           patch --ignore-whitespace -d /opt/homebrew/lib/python3.10/site-packages/dmgbuild -N -p0 < ./utils/build/macos/dmgbuild.patch
+      - uses: Tiryoh/gha-jobid-action@v1
+        id: get_job_id
+        with:
+          job_name: "Build Universal ChimeraX for macOS / build-mac-universal"
+      - name: Note the run and job IDs on Plato
+        uses: ./utils/ci/nightly_logs
+        with:
+          platform: mac_universal
+          deploy_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+          run_id: ${{ github.run_id }}
+          job_id: ${{ steps.get_job_id.outputs.job_id }}
+          build_type: daily
       - uses: ./utils/ci/download_mac_chimerax
         with:
           cache_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
@@ -60,6 +72,11 @@ jobs:
       - name: Make the universal build
         run: |
           python3.10 ./utils/build/macos/make_universal.py chimerax_arm64.app chimerax_intel.app ChimeraX.app 2>&1
+      # Local machines keep the executable bits on these files. Runner machines for whatever reason do not.
+      # Perhaps they are quarantined? al2co doesn't have this problem?
+      - name: Make ambertools executable
+        run: |
+          chmod +x ChimeraX.app/Contents/bin/amber*/bin/*
       - name: Remove unneeded ChimeraXes
         run: |
           rm -r chimerax_arm64.app

diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
@@ -2,7 +2,7 @@ name: Nightly Build
 on:
   workflow_dispatch:
   schedule:
-    - cron: "0 8 * * *" # 8AM UTC / 12AM PST / 1AM PDT
+    - cron: "0 7 * * *" # 7AM UTC / 11PM PST / 12AM PDT
 
 jobs:
   build-rocky8-docker:

diff --git a/.github/workflows/rocky8_build.yml b/.github/workflows/rocky8_build.yml
@@ -37,6 +37,18 @@ jobs:
           platform: linux
           architecture: x86_64
           cache_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+      - uses: Tiryoh/gha-jobid-action@v1
+        id: get_job_id
+        with:
+          job_name: "Build ChimeraX for Rocky 8 / Build ChimeraX for Rocky 8"
+      - name: Note the run and job IDs on Plato
+        uses: ./utils/ci/nightly_logs
+        with:
+          platform: centos-8
+          deploy_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+          run_id: ${{ github.run_id }}
+          job_id: ${{ steps.get_job_id.outputs.job_id }}
+          build_type: daily
       - run: source /opt/rh/gcc-toolset-10/enable && MAKEOPTS="-j$(nproc)" make -j$(nproc) -f Makefile.centos install-rbvi
       - name: Run the legacy test suite
         run: make test

diff --git a/.github/workflows/rocky9_build.yml b/.github/workflows/rocky9_build.yml
@@ -37,6 +37,18 @@ jobs:
           platform: linux
           architecture: x86_64
           cache_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+      - uses: Tiryoh/gha-jobid-action@v1
+        id: get_job_id
+        with:
+          job_name: "Build ChimeraX for Rocky 9 / build-rocky9-docker"
+      - name: Note the run and job IDs on Plato
+        uses: ./utils/ci/nightly_logs
+        with:
+          platform: centos-9
+          deploy_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+          run_id: ${{ github.run_id }}
+          job_id: ${{ steps.get_job_id.outputs.job_id }}
+          build_type: daily
       - name: Restore bundles and includes from cache
         uses: actions/cache/restore@v4
         with:

diff --git a/.github/workflows/ubuntu_build.yml b/.github/workflows/ubuntu_build.yml
@@ -31,6 +31,18 @@ jobs:
           platform: linux
           architecture: x86_64
           cache_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+      - uses: Tiryoh/gha-jobid-action@v1
+        id: get_job_id
+        with:
+          job_name: "Build ChimeraX for Ubuntu / build-ubuntu (${{ matrix.os }})"
+      - name: Note the run and job IDs on Plato
+        uses: ./utils/ci/nightly_logs
+        with:
+          platform: ${{ matrix.os }}
+          deploy_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+          run_id: ${{ github.run_id }}
+          job_id: ${{ steps.get_job_id.outputs.job_id }}
+          build_type: daily
       - name: Restore bundles and includes from cache
         uses: actions/cache/restore@v4
         with:

diff --git a/.github/workflows/windows_build.yml b/.github/workflows/windows_build.yml
@@ -18,7 +18,7 @@ on:
 
 jobs:
   build-test:
-    name: Test
+    name: Windows Build
     if: ${{ inputs.release_type == 'test' }}
     runs-on: windows-latest
     defaults:
@@ -30,7 +30,7 @@ jobs:
         with:
           msystem: MINGW64
           update: true
-          install: git mingw-w64-x86_64-imagemagick mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-gcc-objc mingw-w64-x86_64-gcc-fortran rsync patch unzip openssh make mingw-w64-x86_64-autotools
+          install: git mingw-w64-x86_64-imagemagick mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-gcc-objc mingw-w64-x86_64-gcc-fortran rsync patch unzip openssh make mingw-w64-x86_64-autotools mingw-w64-x86_64-jq
       - run: AUTOMATIC_DISCOVERY=1 . ./vsvars.sh && MAKEOPTS="-j$(nproc)" make -j$(nproc) build-minimal
       - name: Run the legacy test suite
         run: AUTOMATIC_DISCOVERY=1 . ./vsvars.sh && make test
@@ -68,6 +68,18 @@ jobs:
           platform: windows
           architecture: x86
           cache_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+      - uses: Tiryoh/gha-jobid-action@v1
+        id: get_job_id
+        with:
+          job_name: "Build ChimeraX for Windows / Daily"
+      - name: Note the run and job IDs on Plato
+        uses: ./utils/ci/nightly_logs
+        with:
+          platform: windows
+          deploy_key: ${{ secrets.PREBUILT_CACHE_SECRET }}
+          run_id: ${{ github.run_id }}
+          job_id: ${{ steps.get_job_id.outputs.job_id }}
+          build_type: daily
       - run: AUTOMATIC_DISCOVERY=1 . ./vsvars.sh && MAKEOPTS="-j$(nproc)" make -j$(nproc) install
       - name: Run the legacy test suite
         run: AUTOMATIC_DISCOVERY=1 . ./vsvars.sh && make test

diff --git a/docs/devel/tutorials/tutorial_command.rst b/docs/devel/tutorials/tutorial_command.rst
@@ -209,14 +209,14 @@ the array of atoms, their coordinates, and their center of mass by
 calling :py:func:`_get_cofm`.  It then
 
 #. computes the distances from each atom to the center of mass
-   using Numpy (line 88),
+   using Numpy (line 104),
 #. sorts the atom indices by distances so that indices of atoms that
    are closer to the center of mass are towards the front of the
    sort result (:code:`argsort(distances)`), and select the first
-   :code:`count` indices (line 94),
-#. turn the array of indices into an array of atoms (line 97),
+   :code:`count` indices (line 110),
+#. turn the array of indices into an array of atoms (line 113),
    and
-#. finally, set the color of the selected atoms (line 101).
+#. finally, set the color of the selected atoms (line 117).
    The :py:attr:`colors` attribute of the atomic array is an
    Nx4 array of integers, where N is the number of atoms and
    the rows (of 4 elements) are the RGBA values for each atom.
@@ -242,29 +242,27 @@ calling :py:func:`_get_cofm`.  It then
 
 If the user did not choose specific atoms (when :code:`atoms`
 is :code:`None`), the usual ChimeraX interpretation is that all
-atoms should be used (lines 123-125).
-:py:func:`chimerax.core.commands.atomspec.all_objects` returns
-an instance of `chimerax.core.objects.Object` that contains
-all open models in the current ChimeraX session, and whose
-:py:attr:`atoms` attribute is an array of atoms in the included
+atoms should be used (lines 139-141).
+:py:func:`chimerax.atomic.structure.all_atoms` returns
+an array of atoms from all open
 models.  Transformed and untransformed coordinates are accessed
 using the :py:attr:`scene_coords` and :py:attr:`coords` attributes
-of the atom array, respectively (lines 132-135).  If atomic mass
+of the atom array, respectively (lines 148-151).  If atomic mass
 need not be included, the "center of mass" is simply the average
-of the coordinates (line 141); if a weighted calculation is required,
+of the coordinates (line 157); if a weighted calculation is required,
 (a) the atomic masses are retrieved by :code:`atoms.elements.masses`
-(line 143),
+(line 159),
 (b) the coordinates are scaled by the corresponding atomic masses
-(line 144), and
-(c) the weighted average is computed (line 145).
+(line 160), and
+(c) the weighted average is computed (line 161).
 
 For performance, ChimeraX makes use of `NumPy`_ arrays in many contexts.
 The container for atoms is typically a
 :py:class:`chimerax.atomic.molarray.Collection`
 instance, as are those for bonds, residues, and atomic structures.
 Fetching the same attribute, e.g., coordinates, from a collection
 of molecular data, e.g., atoms, usually results in a NumPy array.
-Although code involving NumPy arrays are sometimes opaque, they are
+Although code involving NumPy arrays is sometimes opaque, they are
 typically much more efficient than using Python loops.
 
 .. _command help:

diff --git a/docs/presentations.html b/docs/presentations.html
@@ -39,6 +39,10 @@ <h2>ChimeraX Demonstrations, Talks and Posters</h2>
 <a href="https://rbvi.github.io/chimerax-recipes/">ChimeraX recipes</a>
 </p>
 
+<p>
+<a href="https://www.rbvi.ucsf.edu/chimerax/data/af3-drugs-dec2024/af3_drugs.html">Docking antiviral drugs to Nipah virus, influenza virus and HIV virus proteins using AlphaFold 3</a>. December 18, 2024.
+</p>
+
 <p>
 <a href="https://www.rbvi.ucsf.edu/chimerax/data/af3-wynton-dec2024/alphafold3_wynton.html">How to run AlphaFold 3 on the UCSF Wynton cluster</a>. December 4, 2024.
 </p>

diff --git a/docs/user/tools/profilegrid.html b/docs/user/tools/profilegrid.html
@@ -55,11 +55,23 @@ <h3><a href="../index.html#tools">Tool</a>: Profile Grid</h3>
 in which the rows are the possible sequence characters (residue one-letter
 codes and gap), the columns are positions in the alignment 
 (as in the standard view of a sequence alignment), and the values 
-in the cells are percentages of that type of residue at that position,
+in the cells are the prevalences of that type of residue at that position.
+</p><p>
+<b>Profile Grid</b> is a reimplementation of the viewer developed 
+by Alberto Roca, as described in:
+</p>
+<blockquote>
+<a href="https://bmcproc.biomedcentral.com/articles/10.1186/1753-6561-8-S2-S6"
+target="_blank">
+ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos.</a>
+Roca AI.  <i>BMC Proc.</i> 2014 Aug 28;8(Suppl 2 Proceedings of the 
+3rd Annual Symposium on Biologica):S6.
+</blockquote>
+<p>
+The values in the ChimeraX <b>Profile Grid</b> are percentages
 rounded to the nearest integer. A blank cell means that no sequences
 at all have that residue type at that position, whereas a displayed value
 of 0 means that some do, but &lt;0.5%.
-</p><p>
 Much like the <a href="sequenceviewer.html"><b>Sequence Viewer</b></a>,
 the <b>Profile Grid</b> tool interacts with any 
 <a href="sequenceviewer.html#association">associated</a> structures, and it

diff --git a/mkcentos.py b/mkcentos.py
@@ -120,6 +120,7 @@
         "libglvnd-egl": None,
         "libglvnd-glx": None,
         "libstdc++": None,
+        "libtheora": None,
         "libuuid": None,
         "libwayland-client": None,
         "libwayland-cursor": None,
@@ -181,6 +182,7 @@
         "libglvnd-egl": None,
         "libglvnd-glx": None,
         "libstdc++": None,
+        "libtheora": None,
         "libuuid": None,
         "libwayland-client": None,
         "libwayland-cursor": None,

diff --git a/mkubuntu.py b/mkubuntu.py
@@ -184,6 +184,7 @@
         "libsqlite3-0": "3.31.1",
         "libssl1.1": "1.1.1f",
         "libstdc++6": "10-20200411",
+        "libtheora": None,
         "libtinfo6": "6.2",
         "libuuid1": "2.34",
         "libwayland-client0": "1.18.0",
@@ -254,6 +255,7 @@
         "libsqlite3-0": "3.31.1",
         "libssl3": "3.0.2",
         "libstdc++6": "10-20200411",
+        "libtheora": None,
         "libtinfo6": "6.2",
         "libuuid1": "2.34",
         "libwayland-client0": "1.18.0",
@@ -324,6 +326,7 @@
         "libsqlite3-0": "3.31.1",
         "libssl3": "3.0.2",
         "libstdc++6": "10-20200411",
+        "libtheora": None,
         "libtinfo6": "6.2",
         "libuuid1": "2.34",
         "libwayland-client0": "1.18.0",

diff --git a/prereqs/Makefile b/prereqs/Makefile
@@ -56,7 +56,7 @@ endif
 .NOTPARALLEL:
 
 # keep in alphabetical order, dependencies go below
-SUBDIRS	+= ambertools openmm pips PyQt Python
+SUBDIRS	+= ambertools pips PyQt Python
 
 
 # All needed subdirectories must be set by now.
-Original file line number
+Diff line change
@@ Expand Up / @@ -39,6 +39,10 @@ <h2>ChimeraX Demonstrations, Talks and Posters</h2> @@
     <a href="https://rbvi.github.io/chimerax-recipes/">ChimeraX recipes</a>
     </p>
+    <p>
+    <a href="https://www.rbvi.ucsf.edu/chimerax/data/af3-drugs-dec2024/af3_drugs.html">Docking antiviral drugs to Nipah virus, influenza virus and HIV virus proteins using AlphaFold 3</a>. December 18, 2024.
+    </p>
     <p>
     <a href="https://www.rbvi.ucsf.edu/chimerax/data/af3-wynton-dec2024/alphafold3_wynton.html">How to run AlphaFold 3 on the UCSF Wynton cluster</a>. December 4, 2024.
     </p>
@@ Expand Down @@