Initial import

build_tools/capture_stats.sh

@@ -0,0 +1,7 @@
+git log|grep Author| awk -F: '{print $2;}' | sed 's%\([ ]*\)\(.*\)<.*>\([ ]*\)%\2%g' |sort|uniq | \
+  (
+    while read; do
+	n=$(git log | grep Author | grep "$REPLY" | wc | awk '{print $1;}' )
+	echo "'$REPLY' $n"
+    done
+  )

build_tools/gather_sources.py

@@ -0,0 +1,243 @@
+#+
+#   ARES/HADES/BORG Package -- ./build_tools/gather_sources.py
+#   Copyright (C) 2014-2020 Guilhem Lavaux <guilhem.lavaux@iap.fr>
+#
+#   Additional contributions from:
+#      Guilhem Lavaux <guilhem.lavaux@iap.fr> (2023)
+#   
+#+
+# ARES TAG: authors_num = 1
+# ARES TAG: name(0) = Guilhem Lavaux
+# ARES TAG: email(0) = guilhem.lavaux@iap.fr
+# ARES TAG: year(0) = 2014-2020
+import sys
+import shutil
+import tempfile
+import re
+import time
+from git import Repo,Tree,Blob,Submodule
+
+distribute_text=""
+
+def build_slice(start, end):
+  if end == start:
+    return str(start)
+  else:
+    return str(start)+"-"+str(end)
+
+def line_injection(tag, text, func):
+  output = []
+  for line in text.split('\n'):
+    if line.find(tag) >= 0:
+      line = func(line)
+    output.append(line)
+  return "\n".join(output)
+
+def build_years(years):
+  year_list = []
+  start = prev_y = years[0]
+  for y in years[1:]:
+    if y != prev_y+1:
+      year_list.append(build_slice(start, prev_y))
+      start = y
+    prev_y = y
+  year_list.append(build_slice(start, prev_y))
+
+  return ", ".join(year_list) #[str(y) for y in years])
+
+class BadFileData(Exception):
+  pass
+
+def checked_author(data, i):
+  defaults = {
+     'name(0)': 'Guilhem Lavaux',
+     'email(0)': 'guilhem.lavaux@iap.fr',
+     'year(0)': '2014-2020',
+     'name(1)': 'Jens Jasche',
+     'email(1)': 'jens.jasche@fysik.su.se',
+     'year(1)': '2009-2020'
+  }
+  codes = ['name(%d)' % i, 'email(%d)' % i, 'year(%d)' % i]
+  if any(not s in data for s in codes):
+    if i <= 1:
+      print("   \033[1mWARNING: Using default author data. Please fix file.\033[0m")
+    else:
+      print("   \033[41mERROR: Need more author data. Please fix file.\033[0m")
+      raise BadFileData()
+
+  defaults.update(data)
+  return tuple(map(lambda k: defaults[k], codes))
+
+def main_author_handler(line, data, fname):
+  num = int(data.get('authors_num', 2))
+  output = []
+  for i in range(num):
+     name, email, year = checked_author(data, i)
+     this_line = re.sub('@MAIN_NAME@', name, line)
+     this_line = re.sub('@MAIN_EMAIL@', email, this_line)
+     output.append( re.sub('@MAIN_YEAR@', year, this_line) )
+  return "\n".join(output)
+
+discard_set = set(['Temp'])
+
+def apply_license(license, relimit, filename, authors):
+  header = re.sub(r'@FILENAME@', filename, license)
+  # Look for the AUTHORS tag in the license template, it has to be support both type of comment.
+  m = re.search(
+      r'^([@#/<>()\w\-*+ \t\n:.]+)\n([#/()\w\-* \t]*)@AUTHORS@([#/()\w\-* \t]*)\n([@#/()\w\-*+ \n:.;,<>]+)$',
+      header, flags=re.MULTILINE)
+  init_header,pre_author,post_author,final_header = m.group(1,2,3,4)
+  header = init_header + '\n'
+  author_list = list( authors.keys())
+  author_list.sort()
+  for author in author_list:
+    if author in discard_set:
+      continue
+    a_data = authors[author]
+    email = a_data['email']
+    years = a_data['years']
+    years = build_years(years)
+    header += pre_author + ("%(name)s <%(email)s> (%(years)s)" % dict(name=author,email=email, years=years)) + post_author + '\n'
+  header += final_header
+
+  m = re.search(
+      r'^([@#/<>(),\w\-*+ \t\n:.]+)\n([#/()\w\-* \t]*)@DISTRIBUTE@([#/()\w\-* \t]*)\n([@#/()\w\-*+ \n:.;,<>]+)$',
+      header, flags=re.MULTILINE)
+  if m is None:
+     print("We reached an invalid state.")
+     print(f"Header is:\n{header}")
+     sys.exit(1)
+  init_header,pre_distribute,post_distribute,final_header = m.group(1,2,3,4)
+  header = f"{init_header}\n"
+  for distribute_line in distribute_text.split('\n'):
+    header += f"{pre_distribute}{distribute_line}{post_distribute}\n"
+  header += final_header
+
+  with open(filename, mode="rt", encoding="UTF-8") as f:
+      lines = f.read()
+
+  # Now look for the tag section
+  specials = {}
+  for a in re.finditer(r"(#|//) ARES TAG:[ \t]*(?P<tag>[\w()]+)[ \t]*=[ \t]*(?P<value>[\w\t \-_\.@]*)", lines):
+    b = a.groupdict()
+    specials[b['tag']] = b['value']
+
+  header = line_injection('@MAIN_NAME@', header, lambda l: main_author_handler(l, specials, filename))
+
+  lines = re.sub(relimit, lambda x: (("" if x.group(1) is None else x.group(1)) + header), lines)
+
+  with tempfile.NamedTemporaryFile(delete=False,encoding="UTF-8",mode="wt") as tmp_sources:
+    tmp_sources.write(lines)
+
+  shutil.move(tmp_sources.name, filename)
+
+def apply_python_license(filename, authors):
+  license="""#+
+#   ARES/HADES/BORG Package -- @FILENAME@
+#   Copyright (C) @MAIN_YEAR@ @MAIN_NAME@ <@MAIN_EMAIL@>
+#
+#   Additional contributions from:
+#      @AUTHORS@
+#   @DISTRIBUTE@
+#+
+"""
+
+  print("Shell/Python/Julia file: %s" % filename)
+  relimit=r'^(#!.*\n)?#\+\n(#.*\n)*#\+\n'
+  apply_license(license, relimit, filename, authors)
+
+
+def apply_cpp_license(filename, authors):
+  license="""/*+
+    ARES/HADES/BORG Package -- @FILENAME@
+    Copyright (C) @MAIN_YEAR@ @MAIN_NAME@ <@MAIN_EMAIL@>
+
+    Additional contributions from:
+       @AUTHORS@
+    @DISTRIBUTE@
++*/
+"""
+  relimit = r'(?s)^()/\*\+.*\+\*/\n'
+  print("C++ file: %s" % filename)
+  apply_license(license, relimit, filename, authors)
+
+
+def patch_author_list(authors):
+  patcher={
+     'Guilhem Lavaux':'guilhem.lavaux@iap.fr',
+     'Jens Jasche':'j.jasche@tum.de'}
+  for a in patcher.keys():
+    if a in authors:
+      data = authors[a]
+      data['email'] = patcher[a]
+
+  author_merge(authors, 'MinhMPA', 'Minh Nguyen')
+  author_merge(authors, 'Minh MPA', 'Minh Nguyen')
+  author_merge(authors, 'flo', 'Florian Führer')
+  author_merge(authors, 'LAVAUX Guilhem', 'Guilhem Lavaux')
+
+def author_merge(authors, a_from, a_to):
+  if a_from in authors:
+    data1 = authors[a_from]
+    del authors[a_from]
+    if a_to in authors:
+      data2 = authors[a_to]
+      s = set(data2['years'])
+      for y in data1['years']:
+        s.add(y)
+      s = list(s)
+      s.sort()
+      data2['years'] = s
+    else:
+      authors[a_to] = data1
+
+def check_authors(repo, fname):
+  authors={}
+  author_names={}
+  for c,_ in repo.blame('HEAD',fname,w=True,M=True):
+    if not c.author.name in authors:
+      authors[c.author.name] = set()
+    author_names[c.author.name] = c.author.email
+    authors[c.author.name].add(time.gmtime(c.authored_date)[0])
+
+  for k in authors.keys():
+    authors[k] = list(authors[k])
+    authors[k].sort()
+
+  authors = {k:dict(email=author_names[k],years=authors[k]) for k in authors.keys()}
+  patch_author_list(authors)
+  return authors
+
+def manage_file(repo, fname):
+  authors = check_authors(repo, fname)
+  if re.match(".*\.(sh|py|pyx|jl)$",fname) != None:
+    apply_python_license(fname, authors)
+  if re.match('.*\.(tcc|cpp|hpp|h)$', fname) != None:
+    apply_cpp_license(fname, authors)
+
+def analyze_tree(repo, prefix, t):
+  for entry in t:
+    if type(entry) == Submodule:
+#      analyze_tree(prefix + "/" + entry.path, Repo(entry.path).tree())
+#entry.module())
+      print("Seeing a submodule at path " + entry.path)
+      continue
+    ename = entry.name
+    if ename == 'external' or ename == 'cmake_modules':
+      continue
+    if type(entry) == Tree:
+      analyze_tree(repo, prefix + "/" + ename, entry)
+    elif type(entry) == Blob:
+      fname=prefix+"/"+ename
+      manage_file(repo, fname)
+
+
+if __name__=="__main__":
+  repo = Repo(".")
+  assert repo.bare == False
+  if len(sys.argv) > 1:
+     for f in sys.argv[1:]:
+        manage_file(repo, f)
+  else:
+     t = repo.tree()
+     analyze_tree(repo, ".", t)

build_tools/gen_code_in_header.py

@@ -0,0 +1,20 @@
+#+
+#   ARES/HADES/BORG Package -- ./build_tools/gen_code_in_header.py
+#   Copyright (C) 2014-2020 Guilhem Lavaux <guilhem.lavaux@iap.fr>
+#   Copyright (C) 2009-2020 Jens Jasche <jens.jasche@fysik.su.se>
+#
+#   Additional contributions from:
+#      Guilhem Lavaux <guilhem.lavaux@iap.fr> (2023)
+#   
+#+
+import sys
+import re
+
+code=""
+with open(sys.argv[1], mode="r") as f_in, open(sys.argv[2], mode="w") as f_out:
+  for line in f_in:
+    line = re.sub(r'\\', r'\\\\', line)
+    line = re.sub(r'"', r'\"', line)
+    line = line[:-1]
+    code += line + "\\n"
+  f_out.write('"%s"' % (code,))

build_tools/gen_splash.py

@@ -0,0 +1,21 @@
+#+
+#   ARES/HADES/BORG Package -- ./build_tools/gen_splash.py
+#   Copyright (C) 2014-2020 Guilhem Lavaux <guilhem.lavaux@iap.fr>
+#   Copyright (C) 2009-2020 Jens Jasche <jens.jasche@fysik.su.se>
+#
+#   Additional contributions from:
+#      Guilhem Lavaux <guilhem.lavaux@iap.fr> (2023)
+#   
+#+
+import sys
+import re
+
+prev_line=None
+with open(sys.argv[1], mode="r") as f_in, open(sys.argv[2], mode="w") as f_out:
+  for line in f_in:
+    if prev_line is not None:
+      f_out.write('"' + prev_line + '",\n')
+    line = re.sub(r'\\', r'\\\\', line)
+    line = re.sub(r'"', r'\"', line)
+    prev_line = line[:-1]
+  f_out.write('"' + prev_line + '"\n')

build_tools/python-builder/Dockerfile

@@ -0,0 +1,20 @@
+#FROM quay.io/pypa/manylinux2014_x86_64
+FROM quay.io/pypa/manylinux2010_x86_64
+ARG CMAKE=3.17.3
+
+RUN yum install -y git && \
+   ( \
+      git clone git://github.com/ninja-build/ninja.git && \
+      cd ninja && \
+      /opt/python/cp36-cp36m/bin/python3 ./configure.py --bootstrap && \
+      ./ninja && cp ninja /usr/bin \
+   ) && rm -fr ninja && yum clean all
+
+RUN \ 
+  yum install -y wget openssl-devel &&  \
+  wget https://github.com/Kitware/CMake/releases/download/v${CMAKE}/cmake-${CMAKE}.tar.gz && \
+  tar zxvf cmake-${CMAKE}.tar.gz  && \
+  ( \
+     cd cmake-${CMAKE} &&  ./bootstrap && make -j4 && make install \
+  ) && rm -fr cmake-${CMAKE}* && \
+  yum clean all

build_tools/python-builder/build-wheels.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+set -e -x
+
+# Install a system package required by our library
+#yum install -y atlas-devel
+yum install -y  zlib-devel
+
+ln -fs /usr/local/bin/cmake /usr/bin/cmake
+
+
+ALL_PYTHON="cp36-cp36m" # cp37-cp37m cp38-cp38" 
+
+# Compile wheels
+for pkg in $ALL_PYTHON; do
+    PYBIN=/opt/python/${pkg}/bin
+#    "${PYBIN}/pip" install -r /io/dev-requirements.txt
+    "${PYBIN}/pip" install -r /io/requirements.txt
+    "${PYBIN}/pip" wheel -vvv /io/ -w wheelhouse/
+done
+
+rm -f wheelhouse/numpy*
+
+# Bundle external shared libraries into the wheels
+for whl in wheelhouse/*.whl; do
+    auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/
+done
+
+# Install packages and test
+for pkg in $ALL_PYTHON; do
+    PYBIN=/opt/python/${pkg}/bin
+    "${PYBIN}/pip" install pyborg --no-index -f /io/wheelhouse
+done

build_tools/python-builder/start.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+d=$(pwd)
+if test x"$(basename $d)" = xbuilder; then
+  d=${d}/../
+fi
+if ! [ -e ${d}/setup.py ] ; then
+  echo "Unknown directory. Please move to the root of cosmotool source tree."
+  exit 1
+fi
+
+#podman run -ti  --rm -e PLAT=manylinux2014_x86_64 -v ${d}:/io:Z pip-builder /io/builder/build-wheels.sh
+podman run -ti  --rm -e PLAT=manylinux2010_x86_64 -v ${d}:/io:Z pip-builder /io/builder/build-wheels.sh