Seq dependency removed

README.md

@@ -13,15 +13,19 @@ mkdir $HOME/.codon && curl -L https://github.com/exaloop/codon/releases/download
 
 Then install Sequre:
 ```bash
-curl -L https://github.com/0xTCG/sequre/releases/download/v0.0.16-alpha/sequre-$(uname -s | awk '{print tolower($0)}')-$(uname -m).tar.gz | tar zxvf - -C $HOME/.codon/lib/codon/plugins
+curl -L https://github.com/0xTCG/sequre/releases/download/v0.0.20-alpha/sequre-$(uname -s | awk '{print tolower($0)}')-$(uname -m).tar.gz | tar zxvf - -C $HOME/.codon/lib/codon/plugins
 ```
 
 Afterwards, add alias for sequre command:
 ```bash
-alias sequre="find . -name 'sock.*' -exec rm {} \; && $HOME/.codon/bin/codon run --disable-opt="core-pythonic-list-addition-opt" -plugin sequre -plugin seq"
+alias sequre="find . -name 'sock.*' -exec rm {} \; && CODON_DEBUG=lt $HOME/.codon/bin/codon run --disable-opt="core-pythonic-list-addition-opt" -plugin sequre"
 ```
 
-Finally, you can run Sequre as:
+Finally, clone the repository:
+```bash
+git clone https://github.com/0xTCG/sequre.git && cd sequre
+```
+and run Sequre examples:
 ```bash
 sequre examples/local_run.codon
 ```
@@ -38,7 +42,7 @@ SEQURE_CP_IPS=<ip1>,<ip2>,...,<ipN> sequre examples/online_run.codon <pid>
 ```
 where `<ipN>` denotes the IP address of each party and `<pid>` denotes the ID of the party.
 
-For example, in a two-party setup with a trusted dealer, run:
+For example, in a two-party setup with a trusted dealer, run (IP addresses are random):
 ```bash
 SEQURE_CP_IPS=192.168.0.1,192.168.0.2,192.168.0.3 sequre examples/online_run.codon 0
 ```
@@ -54,8 +58,6 @@ SEQURE_CP_IPS=192.168.0.1,192.168.0.2,192.168.0.3 sequre examples/online_run.cod
 ```
 at the second party (CP2).
 
-(IP addresses are fictional)
-
 ### Local run
 
 To simulate the run on a single machine over multiple processes run:
@@ -78,31 +80,20 @@ sequre -release examples/local_run.codon --skip-mhe-setup
 
 ## Benchmarks (USENIX Security 2025)
 
-Run all USENIX Security 2025 benchmarks.
-**Note:** We generate all data at random for easier reproducibility. For the original data (from dbGaP under accession phs000716.v1.p1), please consult the authors.
+**Note:** We generate all data at random for easier testing. For the original data (from dbGaP under accession phs000716.v1.p1), please consult the authors.
+
+Run all USENIX Security 2025 benchmarks within the cloned Sequre repository.
 
 ### Local run (single machine)
 ```bash
-CODON_DEBUG=lt scripts/run.sh -release benchmarks --local --jit --stdlib-builtin --king --pca --gwas-without-norm
+sequre -release scripts/invoke.codon run-benchmarks --local --jit --stdlib-builtin --king --pca --gwas-without-norm
 ```
 
 ### Online run
 Set each `<ipN>` to the respective IP address and `<pid>` to the respective ID. Please see the [online run example above](online_run).
 
 ```bash
-CODON_DEBUG=lt  SEQURE_CP_IPS=<ip1>,<ip2>,...,<ipN> scripts/run.sh -release benchmarks --local --jit --stdlib-builtin --king --pca --gwas-without-norm <pid>
-```
-
-### Via docker (local run)
-```bash
-mkdir -p results && sudo podman run --mount type=bind,source=$(pwd)/results,destination=/sequre/results --security-opt label=disable -e "CODON_DEBUG=lt" --privileged --rm -t hsmile/shechi:usenix scripts/run.sh -release benchmarks --local --jit --stdlib-builtin --king --pca --gwas-without-norm
-```
-
-### Via docker (online run)
-Set each `<ipN>` to the respective IP address and `<pid>` to the respective ID. Please see the [online run example above](online_run). Also, map as many ports as the number of connections in the network (i.e. (N * (N - 1)) / 2) where N is the number of parties (including trusted dealer) starting from port 9001.
-
-```bash
-mkdir -p results && sudo podman run --mount type=bind,source=$(pwd)/results,destination=/sequre/results --security-opt label=disable -e "CODON_DEBUG=lt" -e "SEQURE_CP_IPS=<ip1>,<ip2>,...,<ipN>" --privileged --rm -p 9001:9001 -p 9002:9002 -p 9003:9003 -t hsmile/shechi:usenix scripts/run.sh -release benchmarks --jit --stdlib-builtin --king --pca --gwas-without-norm <pid>
+SEQURE_CP_IPS=<ip1>,<ip2>,...,<ipN> sequre -release scripts/invoke.codon run-benchmarks --jit --stdlib-builtin --king --pca --gwas-without-norm <pid>
 ```
 
 ### Check accuracy

scripts/run.sh

@@ -37,15 +37,15 @@ echo "Sequre plugin path: $SEQURE_PATH"
 if [[ $* == *--jit* ]]
 then
     echo "Running $2 in $1 mode ..."
-    /usr/bin/time -v $SEQURE_CODON_PATH/build/codon run --disable-opt="core-pythonic-list-addition-opt" -plugin $SEQURE_PATH -plugin $SEQURE_SEQ_PATH $1 scripts/invoke.codon run-$2 ${*:3}
+    /usr/bin/time -v $SEQURE_CODON_PATH/build/codon run --disable-opt="core-pythonic-list-addition-opt" -plugin $SEQURE_PATH $1 scripts/invoke.codon run-$2 ${*:3}
     echo "Cleaning up sockets ..."
     find . -name 'sock.*' -exec rm {} \;
 else
     if [[ $* == *--build* ]]
     then
         rm -f ./sequrex
         echo "Compiling $2 in $1 mode ..."
-        CC=clang CXX=clang++ $SEQURE_CODON_PATH/build/codon build --disable-opt="core-pythonic-list-addition-opt" -plugin $SEQURE_PATH -plugin $SEQURE_SEQ_PATH $1 -o sequrex scripts/invoke.codon
+        CC=clang CXX=clang++ $SEQURE_CODON_PATH/build/codon build --disable-opt="core-pythonic-list-addition-opt" -plugin $SEQURE_PATH $1 -o sequrex scripts/invoke.codon
     fi
 
     if [ ! -f "./sequrex" ]

stdlib/pickler.codon

@@ -1,6 +1,5 @@
 from internal.file import _gz_errcheck
 from internal.gc import sizeof, atomic
-from bio.seq import seq
 
 from C import memcpy(Jar, cobj, int)
 from C import perror(cobj)
@@ -124,21 +123,6 @@ class str:
         _read_raw(jar, p, n, pasteurized)
         return str(p, n)
 
-@extend
-class seq:
-    def __pickle__(self, jar: Jar, pasteurized: bool = True):
-        _write(jar, self.len, pasteurized)
-        if not pasteurized: jar += sizeof(int)
-        _write_raw(jar, self.ptr, abs(self.len), pasteurized)
-
-    def __unpickle__(jar: Jar, pasteurized: bool = True):
-        n = _read(jar, pasteurized, int)
-        if not pasteurized: jar += sizeof(int)
-        m = abs(n)
-        p = Ptr[byte](m)
-        _read_raw(jar, p, m, pasteurized)
-        return seq(p, n)
-
 @extend
 class List:
     def __pickle__(self, jar: Jar, pasteurized: bool = True):

tests/__init__.codon

@@ -10,9 +10,6 @@ from ..applications.gwas import \
     gwas_protocol, \
     gwas_without_norm
 from ..applications.dti import dti_mpc_protocol
-from ..applications.opal import sequre_opal, offline_opal, load_dico, OPAL_TARGET_DICO_LABEL
-from ..applications.ganon import sequre_ganon, offline_ganon, FilterConfig
-
 from ..applications.utils.data_sharing import share_data
 from ..applications.offline.seqan import seqan_ungapped_kmer_encode, load_ibf, bulk_count, \
     _trailing_zeros, query_ibf, seqan_ibf_hash, SEQAN_HASH_SEEDS

tests/benchmark.codon

@@ -13,8 +13,6 @@ from ..applications.mi import benchmark_mi
 from ..applications.king import king
 from ..applications.gwas import gwas_protocol, gwas_without_norm
 from ..applications.dti import dti_mpc_protocol, dti_mhe_protocol
-from ..applications.opal import sequre_opal as opal
-from ..applications.ganon import sequre_ganon as ganon, FilterConfig
 from ..applications.genotype_imputation import genotype_imputation
 from ..applications.utils.data_sharing import share_data
 
@@ -474,31 +472,6 @@ def dti_wrapper(mpc, modulus):
         return dti_mhe_protocol(mpc)
     # return dti_mpc_protocol(mpc, True, modulus, False)
 
-def opal_wrapper(mpc, modulus, coverage):
-    opal(mpc, modulus, coverage)[0]
-
-def ganon_wrapper(mpc, modulus, read_limit):
-    parsed_hierarchy = {
-        "level_1": {
-                "window_size": 0,
-                "kmer_size": 19,
-                "offset": 1,
-                "rel_filter": 1,
-                "abs_filter": 0,
-                "alphabet_size": 5  # the size of the nucleotide alphabeth -- 5 in case of SeqAn's IBF (A,C,G,N,T)
-            }
-        }
-
-    filter_config = FilterConfig(
-        ibf_path="data/ganon/opal_dataset_ibf.bin",
-        map_path="data/ganon/opal_dataset_map.txt",
-        rel_cutoff=0.25,
-        abs_cutoff=0.0,
-        bin_count=63,
-        hash_count=4)
-
-    ganon(mpc, parsed_hierarchy, [filter_config], 'tests/data/opal/test.fragments.fasta', modulus, read_limit)
-
 def ablations_wrapper(mpc, modulus):
     rows_per_partition, cols = 16, 8192
     rows = rows_per_partition * (mpc.comms.number_of_parties - 1)
@@ -674,14 +647,8 @@ def benchmark[TP](mpc, benchmark_toggles: dict, modulus: TP):
         time_frame(mpc, credit_score_wrapper, 'Credit score inference', modulus)
     if benchmark_toggles[RUN_TOGGLES.DTI_FLAG] or run_all:
         time_frame(mpc, dti_wrapper, 'Drug target interaction inference', modulus)
-    if benchmark_toggles[RUN_TOGGLES.OPAL_FLAG] or run_all:
-        time_frame(mpc, opal_wrapper, 'Opal 0.1x', modulus, 0.1)
-        time_frame(mpc, opal_wrapper, 'Opal 15x', modulus, 15)
-    if benchmark_toggles[RUN_TOGGLES.GANON_FLAG] or run_all:
-        time_frame(mpc, ganon_wrapper, 'Ganon', modulus, 100)
     if benchmark_toggles[RUN_TOGGLES.GENOTYPE_IMPUTATION_FLAG] or run_all:
         time_frame(mpc, genotype_imputation_wrapper, 'Genotype imputation', modulus)
-
     if benchmark_toggles[RUN_TOGGLES.ABLATIONS_FLAG] or run_all:
         time_frame(mpc, ablations_wrapper, 'Ablation study', modulus)
 

tests/e2e_tests/__init__.codon

@@ -50,11 +50,3 @@ def test_e2e(mpc, tests_toggles, modulus):
         from test_dti import test_dti
         share_data(mpc, "dti", modulus)
         test_dti(mpc, modulus)
-
-    if tests_toggles[RUN_TOGGLES.OPAL_FLAG] or run_e2e:
-        from test_opal import test_opal
-        test_opal(mpc, modulus)
-
-    if tests_toggles[RUN_TOGGLES.GANON_FLAG] or run_e2e:
-        from test_ganon import test_ganon
-        test_ganon(mpc, modulus)

tests/unit_tests/test_helpers.codon

@@ -1,109 +1,9 @@
-from .. import seqan_ungapped_kmer_encode, load_ibf, bulk_count, \
-    _trailing_zeros, query_ibf, seqan_ibf_hash, SEQAN_HASH_SEEDS
-
 from sequre.utils.testing import assert_eq
 from sequre.utils.utils import __rand_mat
 from sequre.constants import MPC_FIELD_SIZE
 from sequre.utils.io import write_matrix, read_matrix
 
 
-def test_seqan_kmer_encoding():
-    expected_encodings = [
-        1184622173257u,
-        5923110866288u,
-        10542068003319u,
-        14563367360345u,
-        15596377817352u,
-        1687943774261u
-    ]
-
-    encodings = list(seqan_ungapped_kmer_encode(s'ACGNTAGCACGNTAGCACGNTAGC', 5))
-    assert_eq('Seqan k-mer encoding', encodings, expected_encodings)
-
-
-def test_seqan_load_ibf():
-    expected_value = 1566604024869293150u << 1
-    ibf, _, __ = load_ibf('tests/data/ganon/sample_bacteria_raw_ibf.bin', 63)
-
-    assert_eq('Seqan load ibf', ibf[0], expected_value)
-
-
-def test_seqan_ibf_hash():
-    expected_hashes = [
-        [1911488, 350080, 2274880, 3018048],
-        [2308352, 2848960, 130496, 1999168],
-        [167104, 2689728, 381824, 886272],
-        [1529664, 628672, 2485696, 2773312],
-        [2531520, 1445504, 603392, 57472],
-        [2528448, 3995200, 111168, 3011904]
-    ] >> 6
-
-    bin_count = 63
-    ibf, _, __ = load_ibf('tests/data/ganon/sample_bacteria_raw_ibf.bin', bin_count)
-    ibf_hash_count = 4
-    sigma = 5
-    ibf_bin_size = u64(len(ibf))
-    hash_shift = _trailing_zeros(ibf_bin_size)
-
-    encodings = list(seqan_ungapped_kmer_encode(s'ACGNTAGCACGNTAGCACGNTAGC', sigma))
-    hashes = [[seqan_ibf_hash(kmer_encoding, seed, ibf_bin_size, hash_shift) for seed in SEQAN_HASH_SEEDS[:ibf_hash_count]] for kmer_encoding in encodings]
-
-    assert_eq('Seqan IBF hash', hashes, expected_hashes)
-
-
-def test_seqan_query_ibf():
-    expected_queries = [
-        70368752566272u,
-        0u,
-        565148976676864u,
-        33554432u,
-        0u,
-        0u
-    ]
-
-    bin_count = 63
-    ibf, _, __ = load_ibf('tests/data/ganon/sample_bacteria_raw_ibf.bin', bin_count)
-    ibf_hash_count = 4
-    sigma = 5
-    ibf_bin_size = u64(len(ibf))
-    hash_shift = _trailing_zeros(ibf_bin_size)
-
-    queries = [
-        query_ibf(
-            ibf,
-            kmer_encoding,
-            ibf_hash_count,
-            ibf_bin_size,
-            bin_count,
-            hash_shift) for kmer_encoding in seqan_ungapped_kmer_encode(s'ACGNTAGCACGNTAGCACGNTAGC', sigma)]
-
-    assert_eq('Seqan query IBF', queries, expected_queries)
-
-
-def test_seqan_bulk_count():
-    expected_count = [
-        0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,
-        1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,
-        0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,
-        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-    ]
-
-    ibf, _, __ = load_ibf('tests/data/ganon/sample_bacteria_raw_ibf.bin', 63)
-    count = bulk_count(ibf, list(seqan_ungapped_kmer_encode(s'ACGNTAGCACGNTAGCACGNTAGC', 5)), 63, 4)
-
-    assert_eq('Seqan bulk count', count, expected_count)
-
-
-def test_seqan():
-    print(f'Testing SeqAn ... \n')
-
-    test_seqan_kmer_encoding()
-    test_seqan_ibf_hash()
-    test_seqan_load_ibf()
-    test_seqan_query_ibf()
-    test_seqan_bulk_count()
-
-
 def test_io():
     print(f'Testing I/O ... \n')
 
@@ -121,6 +21,5 @@ def test_helpers():
     print(f'Testing helpers ... \n')
 
     test_io()
-    test_seqan()
 
     print(f'Helpers tests passed.\n')