this repo has no description
Merge branch 'ocaml:master' into opam-publish-cudajit.0.5.0
authored by
Lukasz Stafiniak
and committed by
GitHub
347a5774
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packages/camlp5/camlp5.8.03.01/opam
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packages/camlp5/camlp5.8.03.01/opam
···
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opam-version: "2.0"
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synopsis: "Preprocessor-pretty-printer of OCaml"
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description: """
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Camlp5 is a preprocessor and pretty-printer for OCaml programs. It also provides parsing and printing tools.
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As a preprocessor, it allows to:
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extend the syntax of OCaml,
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redefine the whole syntax of the language.
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As a pretty printer, it allows to:
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display OCaml programs in an elegant way,
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convert from one syntax to another,
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check the results of syntax extensions.
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Camlp5 also provides some parsing and pretty printing tools:
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extensible grammars
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extensible printers
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stream parsers and lexers
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pretty print module
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It works as a shell command and can also be used in the OCaml toplevel."""
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maintainer: ["Chet Murthy <chetsky@gmail.com>"]
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authors: ["Daniel de Rauglaudre" "Chet Murthy"]
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license: "BSD-3-Clause"
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homepage: "https://camlp5.github.io"
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doc: "https://camlp5.github.io/doc/html"
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bug-reports: "https://github.com/camlp5/camlp5/issues"
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depends: [
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"ocaml" {>= "4.10" & < "5.04.0" }
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"ocamlfind"
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"camlp-streams" { >= "5.0" }
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"conf-perl"
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"conf-bash" { with-test }
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"camlp5-buildscripts" { >= "0.02" }
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"conf-diffutils" { with-test & (os-distribution = "alpine" | os-distribution = "freebsd" | os-family = "opensuse") }
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"re" { >= "1.11.0" }
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"ounit2" { with-test }
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"pcre2" { with-test }
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"rresult"
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"bos"
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"fmt"
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]
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build: [
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["./configure" "--prefix" prefix "-libdir" lib "-mandir" man]
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[make "-j%{jobs}%" "DEBUG=-g" "world.opt"]
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[make "-j%{jobs}%" "DEBUG=-g" "all"]
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[make "-C" "testsuite" "clean" "all-tests"] { with-test }
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[make "-C" "test" "clean" "all"] { with-test & os != "macos" }
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# [make "-C" "scripts" "clean" "test"] { with-test }
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]
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install: [make "install"]
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conflicts: [
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"ocaml-option-bytecode-only"
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"pa_ppx" { < "0.16" }
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"p5scm" { <= "0.3.1" }
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"matita" { <= "0.99.5" }
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"lablgl" { <= "1.07" }
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]
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x-ci-accept-failures: [ "opensuse-tumbleweed" ]
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dev-repo: "git+https://github.com/camlp5/camlp5.git"
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url {
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src: "https://github.com/camlp5/camlp5/archive/refs/tags/8.03.01.tar.gz"
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checksum: [
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"sha512=144ab15e18673fa485d08cf37c6ba69146db7db4be9e7031e202e0747d922e223396b83881b1d65cf27bedb2115d91e5eb62b5a22e2d57dda838013ebd398ff2"
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]
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}
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packages/molenc/molenc.17.0.1/opam
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packages/molenc/molenc.17.0.1/opam
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opam-version: "2.0"
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authors: "Francois Berenger"
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maintainer: "unixjunkie@sdf.org"
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homepage: "https://github.com/UnixJunkie/molenc"
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bug-reports: "https://github.com/UnixJunkie/molenc/issues"
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dev-repo: "git+https://github.com/UnixJunkie/molenc.git"
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license: "BSD-3-Clause"
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build: ["dune" "build" "-p" name "-j" jobs]
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install: [
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["cp" "bin/molenc_diam.py" "%{bin}%/molenc_diam.py"]
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["cp" "bin/molenc_ph4.py" "%{bin}%/molenc_ph4.py"]
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["cp" "bin/molenc.sh" "%{bin}%/molenc.sh"]
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["cp" "bin/molenc_ligprep.sh" "%{bin}%/molenc_ligprep.sh"]
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["cp" "bin/molenc_common.py" "%{bin}%/molenc_common.py"]
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["cp" "bin/molenc_lean.py" "%{bin}%/molenc_lean.py"]
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["cp" "bin/molenc_lizard.py" "%{bin}%/molenc_lizard.py"]
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["cp" "bin/molenc_scan.py" "%{bin}%/molenc_scan.py"]
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["cp" "bin/molenc_scan.sh" "%{bin}%/molenc_scan.sh"]
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["cp" "bin/molenc_type_atoms.py" "%{bin}%/molenc_type_atoms.py"]
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["cp" "bin/smi2png.py" "%{bin}%/molenc_smi2png.py"]
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["cp" "bin/molenc_smisur.py" "%{bin}%/molenc_smisur.py"]
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["cp" "bin/molenc_panascan.py" "%{bin}%/molenc_panascan.py"]
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["cp" "bin/molenc_scaffold.py" "%{bin}%/molenc_scaffold.py"]
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["cp" "bin/molenc_deepsmi.py" "%{bin}%/molenc_deepsmi.py"]
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["cp" "bin/molenc_lead.py" "%{bin}%/molenc_lead.py"]
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["cp" "bin/molenc_drug.py" "%{bin}%/molenc_drug.py"]
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["cp" "bin/molenc_smi2cansmi.py" "%{bin}%/molenc_smi2cansmi.py"]
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["cp" "bin/molenc_std.py" "%{bin}%/molenc_std.py"]
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["cp" "bin/molenc_padel.py" "%{bin}%/molenc_padel.py"]
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["cp" "bin/molenc_rotbond.py" "%{bin}%/molenc_rotbond.py"]
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["cp" "bin/molenc_mview.py" "%{bin}%/molenc_mview.py"]
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["cp" "bin/molenc_HA.py" "%{bin}%/molenc_HA.py"]
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["cp" "bin/molenc_sdf2smi.py" "%{bin}%/molenc_sdf2smi.py"]
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["cp" "bin/molenc_atoms_filter.py" "%{bin}%/molenc_atoms_filter.py"]
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["cp" "bin/molenc_gpr.py" "%{bin}%/molenc_gpr.py"]
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["cp" "bin/molenc_stable.py" "%{bin}%/molenc_stable.py"]
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["cp" "bin/molenc_thash.py" "%{bin}%/molenc_thash.py"]
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["cp" "bin/molenc_SA.py" "%{bin}%/molenc_SA.py"]
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["cp" "bin/fpscores.pkl.gz" "%{bin}%/fpscores.pkl.gz"] # molenc_SA.py's data
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]
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depends: [
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"batteries" {>= "3.5.0"}
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"bst" {>= "2.0.0"}
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"conf-graphviz"
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"conf-python-3"
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"conf-rdkit"
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"cpm" {>= "9.0.0"}
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"dokeysto"
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"dolog" {>= "5.0.0"}
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"dune" {>= "1.11"}
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"line_oriented" {>= "1.2.0"}
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"minicli" {>= "5.0.0"}
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"ocaml" {>= "5.1.0"}
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"ocamlgraph"
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"parany" {>= "12.1.1"}
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"vector3"
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"pyml" {>= "20211015"}
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]
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available: arch != "arm32" & arch != "x86_32"
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synopsis: "Molecular encoder/featurizer using rdkit and OCaml"
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description: """Chemical fingerprints are lossy encodings of molecules.
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molenc allows to encode molecules using unfolded-counted fingerprints
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(i.e. a potentially very long but sparse vector of positive integers).
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Currently, Faulon fingerprints and atom pairs are supported.
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Currently, atom types are the quadruplet
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(#pi-electrons, element symbol, #HA neighbors, formal charge).
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In the future, pharmacophore features might be supported (a more abstract/fuzzy
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atom typing scheme).
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Bibliography:
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=============
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Faulon, J. L., Visco, D. P., & Pophale, R. S. (2003).
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The signature molecular descriptor.
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1. Using extended valence sequences in QSAR and QSPR studies.
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Journal of chemical information and computer sciences, 43(3), 707-720.
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Carhart, R. E., Smith, D. H., & Venkataraghavan, R. (1985).
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Atom pairs as molecular features in structure-activity studies:
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definition and applications.
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Journal of Chemical Information and Computer Sciences, 25(2), 64-73.
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Kearsley, S. K., Sallamack, S., Fluder, E. M., Andose, J. D., Mosley, R. T., &
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Sheridan, R. P. (1996).
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Chemical similarity using physiochemical property descriptors.
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Journal of Chemical Information and Computer Sciences, 36(1), 118-127.
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OpenSMILES specification. Craig A. James et. al. v1.0 2016-05-15.
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http://opensmiles.org/opensmiles.html
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"""
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url {
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src:
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"https://github.com/UnixJunkie/molenc/archive/refs/tags/v17.0.1.tar.gz"
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checksum: [
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"sha256=dee16015c4088cc4a690bfeb5afc4fe4869540bf7e2a998ae3ca8094023728ae"
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]
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}