Build from scratch fails due to older core wheels

[Tom Goddard]

"make build-from-scratch" fails perhaps because core has multiple wheels in its dist directory.

cd /Users/goddard/ucsf/chimerax/build/sync && env SYSTEM_VERSION_COMPAT=0 /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/python3.9 -I -m pip install --upgrade --upgrade-strategy only-if-needed *.whl
Processing ./ChimeraX_AddCharge-1.2.3-py3-none-any.whl
Processing ./ChimeraX_AddH-2.1.11-py3-none-any.whl
Processing ./ChimeraX_AlignmentAlgorithms-2.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_AlignmentHdrs-3.2.1-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_AlignmentMatrices-2.0-py3-none-any.whl
Processing ./ChimeraX_Alignments-2.5.1-py3-none-any.whl
Processing ./ChimeraX_AlphaFold-1.0-py3-none-any.whl
Processing ./ChimeraX_AltlocExplorer-1.0.2-py3-none-any.whl
Processing ./ChimeraX_AmberInfo-1.0-py3-none-any.whl
Processing ./ChimeraX_Arrays-1.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_AtomSearch-2.0.1-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_Atomic-1.39.5-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_AtomicLibrary-7.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_AxesPlanes-2.1-py3-none-any.whl
Processing ./ChimeraX_BILD-1.0-py3-none-any.whl
Processing ./ChimeraX_BasicActions-1.1.1-py3-none-any.whl
Processing ./ChimeraX_BlastProtein-2.1.1-py3-none-any.whl
Processing ./ChimeraX_BondRot-2.0-py3-none-any.whl
Processing ./ChimeraX_BugReporter-1.0-py3-none-any.whl
Processing ./ChimeraX_BuildStructure-2.7-py3-none-any.whl
Processing ./ChimeraX_Bumps-1.0-py3-none-any.whl
Processing ./ChimeraX_BundleBuilder-1.2-py39-none-any.whl
Processing ./ChimeraX_ButtonPanel-1.0-py3-none-any.whl
Processing ./ChimeraX_CageBuilder-1.0-py3-none-any.whl
Processing ./ChimeraX_CellPack-1.0-py3-none-any.whl
Processing ./ChimeraX_Centroids-1.2-py3-none-any.whl
Processing ./ChimeraX_CheckWaters-1.0-py3-none-any.whl
Processing ./ChimeraX_ChemGroup-2.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_Clashes-2.2.4-py3-none-any.whl
Processing ./ChimeraX_ColorActions-1.0-py3-none-any.whl
Processing ./ChimeraX_ColorGlobe-1.0-py3-none-any.whl
Processing ./ChimeraX_ColorKey-1.5.2-py3-none-any.whl
Processing ./ChimeraX_CommandLine-1.2.3-py3-none-any.whl
Processing ./ChimeraX_ConnectStructure-2.0.1-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_Contacts-1.0-py3-none-any.whl
Processing ./ChimeraX_Core-1.5.dev202206301755-cp39-cp39-macosx_12_0_x86_64.whl
Processing ./ChimeraX_Core-1.5.dev202207051909-cp39-cp39-macosx_12_0_x86_64.whl
Processing ./ChimeraX_CoreFormats-1.1-py3-none-any.whl
Processing ./ChimeraX_Crosslinks-1.0-py3-none-any.whl
Processing ./ChimeraX_Crystal-1.0-py3-none-any.whl
Processing ./ChimeraX_CrystalContacts-1.0-py3-none-any.whl
Processing ./ChimeraX_DataFormats-1.2.2-py3-none-any.whl
Processing ./ChimeraX_Dicom-1.1-py3-none-any.whl
Processing ./ChimeraX_DistMonitor-1.1.6-py3-none-any.whl
Processing ./ChimeraX_Dssp-2.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_EMDB_SFF-1.0-py3-none-any.whl
Processing ./ChimeraX_ExperimentalCommands-1.0-py3-none-any.whl
Processing ./ChimeraX_FileHistory-1.0-py3-none-any.whl
Processing ./ChimeraX_FunctionKey-1.0-py3-none-any.whl
Processing ./ChimeraX_Geometry-1.2-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_Graphics-1.1-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_HKCage-1.3-py3-none-any.whl
Processing ./ChimeraX_Hbonds-2.2.1-py3-none-any.whl
Processing ./ChimeraX_Help-1.2-py3-none-any.whl
Processing ./ChimeraX_IHM-1.1-py3-none-any.whl
Processing ./ChimeraX_IMOD-1.0-py3-none-any.whl
Processing ./ChimeraX_IO-1.0.1-py3-none-any.whl
Processing ./ChimeraX_ImageFormats-1.2-py3-none-any.whl
Processing ./ChimeraX_ItemsInspection-1.0-py3-none-any.whl
Processing ./ChimeraX_Label-1.1.1-py3-none-any.whl
Processing ./ChimeraX_ListInfo-1.1.1-py3-none-any.whl
Processing ./ChimeraX_Log-1.1.5-py3-none-any.whl
Processing ./ChimeraX_LookingGlass-1.1-py3-none-any.whl
Processing ./ChimeraX_MDcrds-2.6-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_MLP-1.1-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_MMTF-2.1-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_Maestro-1.8.1-py3-none-any.whl
Processing ./ChimeraX_Map-1.1-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_MapData-2.0-py3-none-any.whl
Processing ./ChimeraX_MapEraser-1.0-py3-none-any.whl
Processing ./ChimeraX_MapFilter-2.0-py3-none-any.whl
Processing ./ChimeraX_MapFit-2.0-py3-none-any.whl
Processing ./ChimeraX_MapSeries-2.1-py3-none-any.whl
Processing ./ChimeraX_Markers-1.0-py3-none-any.whl
Processing ./ChimeraX_Mask-1.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_MatchMaker-2.0.6-py3-none-any.whl
Processing ./ChimeraX_MedicalToolbar-1.0.1-py3-none-any.whl
Processing ./ChimeraX_Meeting-1.0-py3-none-any.whl
Processing ./ChimeraX_ModelPanel-1.3.4-py3-none-any.whl
Processing ./ChimeraX_ModelSeries-1.0-py3-none-any.whl
Processing ./ChimeraX_Modeller-1.5.6-py3-none-any.whl
Processing ./ChimeraX_Mol2-2.0-py3-none-any.whl
Processing ./ChimeraX_Morph-1.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_MouseModes-1.1-py3-none-any.whl
Processing ./ChimeraX_Movie-1.0-py3-none-any.whl
Processing ./ChimeraX_Neuron-1.0-py3-none-any.whl
Processing ./ChimeraX_Nucleotides-2.0.2-py3-none-any.whl
Processing ./ChimeraX_OpenCommand-1.9-py3-none-any.whl
Processing ./ChimeraX_PDB-2.6.6-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_PDBBio-1.0-py3-none-any.whl
Processing ./ChimeraX_PDBLibrary-1.0.2-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_PDBMatrices-1.0-py3-none-any.whl
Processing ./ChimeraX_PIP-0.1.0-py3-none-any.whl
Processing ./ChimeraX_PickBlobs-1.0-py3-none-any.whl
Processing ./ChimeraX_Positions-1.0-py3-none-any.whl
Processing ./ChimeraX_PresetMgr-1.1-py3-none-any.whl
Processing ./ChimeraX_PubChem-2.1-py3-none-any.whl
Processing ./ChimeraX_RNALayout-1.0-py3-none-any.whl
Processing ./ChimeraX_ReadPbonds-1.0.1-py3-none-any.whl
Processing ./ChimeraX_Registration-1.1-py3-none-any.whl
Processing ./ChimeraX_RemoteControl-1.0-py3-none-any.whl
Processing ./ChimeraX_RenumberResidues-1.1-py3-none-any.whl
Processing ./ChimeraX_ResidueFit-1.0-py3-none-any.whl
Processing ./ChimeraX_RestServer-1.1-py3-none-any.whl
Processing ./ChimeraX_RotamerLibMgr-2.0.1-py3-none-any.whl
Processing ./ChimeraX_RotamerLibsDunbrack-2.0-py3-none-any.whl
Processing ./ChimeraX_RotamerLibsDynameomics-2.0-py3-none-any.whl
Processing ./ChimeraX_RotamerLibsRichardson-2.0-py3-none-any.whl
Processing ./ChimeraX_SDF-2.0-py3-none-any.whl
Processing ./ChimeraX_STL-1.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_SaveCommand-1.5.1-py3-none-any.whl
Processing ./ChimeraX_SchemeMgr-1.0-py3-none-any.whl
Processing ./ChimeraX_Segger-1.0-py3-none-any.whl
Processing ./ChimeraX_Segment-1.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_SelInspector-1.0-py3-none-any.whl
Processing ./ChimeraX_SeqView-2.7.1-py3-none-any.whl
Processing ./ChimeraX_Shape-1.0.1-py3-none-any.whl
Processing ./ChimeraX_Shell-1.0-py3-none-any.whl
Processing ./ChimeraX_Shortcuts-1.1-py3-none-any.whl
Processing ./ChimeraX_ShowAttr-1.0-py3-none-any.whl
Processing ./ChimeraX_ShowSequences-1.0-py3-none-any.whl
Processing ./ChimeraX_SideView-1.0-py3-none-any.whl
Processing ./ChimeraX_Smiles-2.1-py3-none-any.whl
Processing ./ChimeraX_SmoothLines-1.0-py3-none-any.whl
Processing ./ChimeraX_SpaceNavigator-1.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_StdCommands-1.8-py3-none-any.whl
Processing ./ChimeraX_Storm-1.0-py3-none-any.whl
Processing ./ChimeraX_StructMeasure-1.0.1-py3-none-any.whl
Processing ./ChimeraX_Struts-1.0.1-py3-none-any.whl
Processing ./ChimeraX_Surface-1.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_SwapAA-2.0-py3-none-any.whl
Processing ./ChimeraX_SwapRes-2.1.1-py3-none-any.whl
Processing ./ChimeraX_TapeMeasure-1.0-py3-none-any.whl
Processing ./ChimeraX_Test-1.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_Toolbar-1.1.1-py3-none-any.whl
Processing ./ChimeraX_ToolshedUtils-1.2.1-py39-none-any.whl
Processing ./ChimeraX_Tug-1.0-py3-none-any.whl
Processing ./ChimeraX_UI-1.21.1-py3-none-any.whl
Processing ./ChimeraX_UnitCell-1.0-py3-none-any.whl
Processing ./ChimeraX_VIPERdb-1.0-py3-none-any.whl
Processing ./ChimeraX_VTK-1.0-py3-none-any.whl
Processing ./ChimeraX_ViewDockX-1.1.2-py3-none-any.whl
Processing ./ChimeraX_Vive-1.1-py3-none-any.whl
Processing ./ChimeraX_VolumeMenu-1.0-py3-none-any.whl
Processing ./ChimeraX_WavefrontOBJ-1.0-py3-none-any.whl
Processing ./ChimeraX_WebCam-1.0-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_WebServices-1.1.0-py3-none-any.whl
Processing ./ChimeraX_Zone-1.0-py3-none-any.whl
Processing ./ChimeraX_coulombic-1.3.2-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_gltf-1.0-py3-none-any.whl
Processing ./ChimeraX_mmCIF-2.7-cp39-cp39-macosx_10_16_x86_64.whl
Processing ./ChimeraX_uniprot-2.2.1-py3-none-any.whl
ERROR: Cannot install chimerax-core 1.5.dev202206301755 (from /Users/goddard/ucsf/chimerax/build/sync/ChimeraX_Core-1.5.dev202206301755-cp39-cp39-macosx_12_0_x86_64.whl) and chimerax-core 1.5.dev202207051909 (from /Users/goddard/ucsf/chimerax/build/sync/ChimeraX_Core-1.5.dev202207051909-cp39-cp39-macosx_12_0_x86_64.whl) because these package versions have conflicting dependencies.

The conflict is caused by:
    The user requested chimerax-core 1.5.dev202206301755 (from /Users/goddard/ucsf/chimerax/build/sync/ChimeraX_Core-1.5.dev202206301755-cp39-cp39-macosx_12_0_x86_64.whl)
    The user requested chimerax-core 1.5.dev202207051909 (from /Users/goddard/ucsf/chimerax/build/sync/ChimeraX_Core-1.5.dev202207051909-cp39-cp39-macosx_12_0_x86_64.whl)

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies
WARNING: You are using pip version 21.3.1; however, version 22.1.2 is available.
You should consider upgrading via the '/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/python3.9 -m pip install --upgrade pip' command.
make[3]: *** [install] Error 1
make[2]: *** [bundles.install] Error 2
make[1]: *** [install] Error 2
make: *** [build-from-scratch] Error 2

[Zach Pearson]

​Made 'make clean' actually clean things, both in the top-level and in the core.