Merge branch 'ocaml:master' into opam-publish-cudajit.0.5.0

packages/camlp5/camlp5.8.03.01/opam

@@ -0,0 +1,67 @@
+
+opam-version: "2.0"
+synopsis: "Preprocessor-pretty-printer of OCaml"
+description: """
+Camlp5 is a preprocessor and pretty-printer for OCaml programs. It also provides parsing and printing tools.
+
+As a preprocessor, it allows to:
+
+extend the syntax of OCaml,
+redefine the whole syntax of the language.
+As a pretty printer, it allows to:
+
+display OCaml programs in an elegant way,
+convert from one syntax to another,
+check the results of syntax extensions.
+Camlp5 also provides some parsing and pretty printing tools:
+
+extensible grammars
+extensible printers
+stream parsers and lexers
+pretty print module
+It works as a shell command and can also be used in the OCaml toplevel."""
+maintainer: ["Chet Murthy <[email protected]>"]
+authors: ["Daniel de Rauglaudre" "Chet Murthy"]
+license: "BSD-3-Clause"
+homepage: "https://camlp5.github.io"
+doc: "https://camlp5.github.io/doc/html"
+bug-reports: "https://github.com/camlp5/camlp5/issues"
+depends: [
+  "ocaml" {>= "4.10" & < "5.04.0" }
+  "ocamlfind"
+  "camlp-streams" { >= "5.0" }
+  "conf-perl"
+  "conf-bash" { with-test }
+  "camlp5-buildscripts" { >= "0.02" }
+  "conf-diffutils" { with-test & (os-distribution = "alpine" | os-distribution = "freebsd" | os-family = "opensuse") }
+  "re" { >= "1.11.0" }
+  "ounit2" { with-test }
+  "pcre2" { with-test }
+  "rresult"
+  "bos"
+  "fmt"
+]
+build: [
+  ["./configure" "--prefix" prefix "-libdir" lib "-mandir" man]
+  [make "-j%{jobs}%" "DEBUG=-g" "world.opt"]
+  [make "-j%{jobs}%" "DEBUG=-g" "all"]
+  [make "-C" "testsuite" "clean" "all-tests"] { with-test }
+  [make "-C" "test" "clean" "all"] { with-test & os != "macos" }
+#  [make "-C" "scripts" "clean" "test"] { with-test }
+]
+install: [make "install"]
+conflicts: [
+   "ocaml-option-bytecode-only"
+   "pa_ppx" { < "0.16" }
+   "p5scm" { <= "0.3.1" }
+   "matita" { <= "0.99.5" }
+   "lablgl" { <= "1.07" }
+]
+x-ci-accept-failures: [ "opensuse-tumbleweed" ]
+dev-repo: "git+https://github.com/camlp5/camlp5.git"
+url {
+  src: "https://github.com/camlp5/camlp5/archive/refs/tags/8.03.01.tar.gz"
+  checksum: [
+    "sha512=144ab15e18673fa485d08cf37c6ba69146db7db4be9e7031e202e0747d922e223396b83881b1d65cf27bedb2115d91e5eb62b5a22e2d57dda838013ebd398ff2"
+  ]
+}

packages/molenc/molenc.17.0.1/opam

@@ -0,0 +1,99 @@
+opam-version: "2.0"
+authors: "Francois Berenger"
+maintainer: "[email protected]"
+homepage: "https://github.com/UnixJunkie/molenc"
+bug-reports: "https://github.com/UnixJunkie/molenc/issues"
+dev-repo: "git+https://github.com/UnixJunkie/molenc.git"
+license: "BSD-3-Clause"
+build: ["dune" "build" "-p" name "-j" jobs]
+install: [
+  ["cp" "bin/molenc_diam.py" "%{bin}%/molenc_diam.py"]
+  ["cp" "bin/molenc_ph4.py" "%{bin}%/molenc_ph4.py"]
+  ["cp" "bin/molenc.sh" "%{bin}%/molenc.sh"]
+  ["cp" "bin/molenc_ligprep.sh" "%{bin}%/molenc_ligprep.sh"]
+  ["cp" "bin/molenc_common.py" "%{bin}%/molenc_common.py"]
+  ["cp" "bin/molenc_lean.py" "%{bin}%/molenc_lean.py"]
+  ["cp" "bin/molenc_lizard.py" "%{bin}%/molenc_lizard.py"]
+  ["cp" "bin/molenc_scan.py" "%{bin}%/molenc_scan.py"]
+  ["cp" "bin/molenc_scan.sh" "%{bin}%/molenc_scan.sh"]
+  ["cp" "bin/molenc_type_atoms.py" "%{bin}%/molenc_type_atoms.py"]
+  ["cp" "bin/smi2png.py" "%{bin}%/molenc_smi2png.py"]
+  ["cp" "bin/molenc_smisur.py" "%{bin}%/molenc_smisur.py"]
+  ["cp" "bin/molenc_panascan.py" "%{bin}%/molenc_panascan.py"]
+  ["cp" "bin/molenc_scaffold.py" "%{bin}%/molenc_scaffold.py"]
+  ["cp" "bin/molenc_deepsmi.py" "%{bin}%/molenc_deepsmi.py"]
+  ["cp" "bin/molenc_lead.py" "%{bin}%/molenc_lead.py"]
+  ["cp" "bin/molenc_drug.py" "%{bin}%/molenc_drug.py"]
+  ["cp" "bin/molenc_smi2cansmi.py" "%{bin}%/molenc_smi2cansmi.py"]
+  ["cp" "bin/molenc_std.py" "%{bin}%/molenc_std.py"]
+  ["cp" "bin/molenc_padel.py" "%{bin}%/molenc_padel.py"]
+  ["cp" "bin/molenc_rotbond.py" "%{bin}%/molenc_rotbond.py"]
+  ["cp" "bin/molenc_mview.py" "%{bin}%/molenc_mview.py"]
+  ["cp" "bin/molenc_HA.py" "%{bin}%/molenc_HA.py"]
+  ["cp" "bin/molenc_sdf2smi.py" "%{bin}%/molenc_sdf2smi.py"]
+  ["cp" "bin/molenc_atoms_filter.py" "%{bin}%/molenc_atoms_filter.py"]
+  ["cp" "bin/molenc_gpr.py" "%{bin}%/molenc_gpr.py"]
+  ["cp" "bin/molenc_stable.py" "%{bin}%/molenc_stable.py"]
+  ["cp" "bin/molenc_thash.py" "%{bin}%/molenc_thash.py"]
+  ["cp" "bin/molenc_SA.py" "%{bin}%/molenc_SA.py"]
+  ["cp" "bin/fpscores.pkl.gz" "%{bin}%/fpscores.pkl.gz"] # molenc_SA.py's data
+]
+depends: [
+  "batteries" {>= "3.5.0"}
+  "bst" {>= "2.0.0"}
+  "conf-graphviz"
+  "conf-python-3"
+  "conf-rdkit"
+  "cpm" {>= "9.0.0"}
+  "dokeysto"
+  "dolog" {>= "5.0.0"}
+  "dune" {>= "1.11"}
+  "line_oriented" {>= "1.2.0"}
+  "minicli" {>= "5.0.0"}
+  "ocaml" {>= "5.1.0"}
+  "ocamlgraph"
+  "parany" {>= "12.1.1"}
+  "vector3"
+  "pyml" {>= "20211015"}
+]
+available: arch != "arm32" & arch != "x86_32"
+synopsis: "Molecular encoder/featurizer using rdkit and OCaml"
+description: """Chemical fingerprints are lossy encodings of molecules.
+molenc allows to encode molecules using unfolded-counted fingerprints
+(i.e. a potentially very long but sparse vector of positive integers).
+
+Currently, Faulon fingerprints and atom pairs are supported.
+
+Currently, atom types are the quadruplet
+(#pi-electrons, element symbol, #HA neighbors, formal charge).
+In the future, pharmacophore features might be supported (a more abstract/fuzzy
+atom typing scheme).
+
+Bibliography:
+=============
+
+Faulon, J. L., Visco, D. P., & Pophale, R. S. (2003).
+The signature molecular descriptor.
+1. Using extended valence sequences in QSAR and QSPR studies.
+Journal of chemical information and computer sciences, 43(3), 707-720.
+
+Carhart, R. E., Smith, D. H., & Venkataraghavan, R. (1985).
+Atom pairs as molecular features in structure-activity studies:
+definition and applications.
+Journal of Chemical Information and Computer Sciences, 25(2), 64-73.
+
+Kearsley, S. K., Sallamack, S., Fluder, E. M., Andose, J. D., Mosley, R. T., &
+Sheridan, R. P. (1996).
+Chemical similarity using physiochemical property descriptors.
+Journal of Chemical Information and Computer Sciences, 36(1), 118-127.
+
+OpenSMILES specification. Craig A. James et. al. v1.0 2016-05-15.
+http://opensmiles.org/opensmiles.html
+"""
+url {
+  src:
+    "https://github.com/UnixJunkie/molenc/archive/refs/tags/v17.0.1.tar.gz"
+  checksum: [
+    "sha256=dee16015c4088cc4a690bfeb5afc4fe4869540bf7e2a998ae3ca8094023728ae"
+  ]
+}